| San Diego International → San Francisco International SAN–SFO | 7,121 | 810,410 | 81% | 447 | United Air Lines Inc., Southwest Airlines Co., SkyWest Airlines Inc., Horizon Air +4 | Jan 2025 – Jul 2026 |
| San Diego International → Harry Reid International SAN–LAS | 6,463 | 640,755 | 74% | 258 | Southwest Airlines Co., SkyWest Airlines Inc., Horizon Air, Frontier Airlines Inc. +4 | Jan 2025 – Jul 2026 |
| San Diego International → Phoenix Sky Harbor International SAN–PHX | 6,426 | 710,910 | 72% | 304 | Southwest Airlines Co., American Airlines Inc., Horizon Air, SkyWest Airlines Inc. +7 | Jan 2025 – Jul 2026 |
| San Diego International → Denver International SAN–DEN | 5,984 | 820,471 | 80% | 853 | Southwest Airlines Co., United Air Lines Inc., Frontier Airlines Inc., Alaska Airlines Inc. +6 | Jan 2025 – Jul 2026 |
| San Diego International → Mineta San Jose International SAN–SJC | 5,543 | 547,964 | 75% | 417 | Southwest Airlines Co., SkyWest Airlines Inc., Horizon Air, Alaska Airlines Inc. +4 | Jan 2025 – Jul 2026 |
| San Diego International → Sacramento International SAN–SMF | 5,530 | 584,022 | 79% | 480 | Southwest Airlines Co., SkyWest Airlines Inc., Horizon Air, Alaska Airlines Inc. +3 | Jan 2025 – Jul 2026 |
| San Diego International → Seattle-Tacoma International SAN–SEA | 4,531 | 620,132 | 83% | 1,050 | Alaska Airlines Inc., Delta Air Lines Inc., Southwest Airlines Co., Horizon Air +2 | Jan 2025 – Jul 2026 |
| San Diego International → Chicago O'Hare International SAN–ORD | 3,777 | 557,542 | 82% | 1,723 | United Air Lines Inc., American Airlines Inc., Alaska Airlines Inc., Frontier Airlines Inc. +3 | Jan 2025 – Jul 2026 |
| San Diego International → Dallas-Fort Worth International SAN–DFW | 3,557 | 581,547 | 86% | 1,171 | American Airlines Inc., Frontier Airlines Inc., Alaska Airlines Inc., Delta Air Lines Inc. +2 | Jan 2025 – Jul 2026 |
| San Diego International → Oakland San Francisco Bay SAN–OAK | 3,505 | 370,533 | 76% | 446 | Southwest Airlines Co., SkyWest Airlines Inc., Federal Express Corporation, Horizon Air +4 | Jan 2025 – Jul 2026 |
| San Diego International → Salt Lake City International SAN–SLC | 3,149 | 385,734 | 82% | 626 | Delta Air Lines Inc., SkyWest Airlines Inc., Southwest Airlines Co., Horizon Air +4 | Jan 2025 – Jul 2026 |
| San Diego International → Austin-Bergstrom International SAN–AUS | 2,563 | 274,652 | 80% | 1,164 | Southwest Airlines Co., SkyWest Airlines Inc., Frontier Airlines Inc., American Airlines Inc. +4 | Jan 2025 – Jul 2026 |
| San Diego International → Los Angeles International SAN–LAX | 2,484 | 145,371 | 71% | 109 | SkyWest Airlines Inc., United Air Lines Inc., Delta Air Lines Inc., Alaska Airlines Inc. +6 | Jan 2025 – Jul 2026 |
| San Diego International → Hartsfield/Jackson Atlanta International SAN–ATL | 2,388 | 405,960 | 88% | 1,892 | Delta Air Lines Inc., Alaska Airlines Inc., Sun Country Airlines d/b/a..., United Air Lines Inc. +1 | Jan 2025 – Jul 2026 |
| San Diego International → John F Kennedy International SAN–JFK | 2,318 | 353,294 | 85% | 2,446 | Delta Air Lines Inc., JetBlue Airways, Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Fresno Yosemite International SAN–FAT | 1,888 | 125,828 | 68% | 314 | SkyWest Airlines Inc., Southwest Airlines Co., Horizon Air, Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → General Edward Lawrence Logan International SAN–BOS | 1,812 | 262,468 | 84% | 2,588 | JetBlue Airways, Alaska Airlines Inc., Delta Air Lines Inc., Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Portland International SAN–PDX | 1,788 | 257,085 | 85% | 933 | Alaska Airlines Inc., Southwest Airlines Co., SkyWest Airlines Inc., Horizon Air +3 | Jan 2025 – Jul 2026 |
| San Diego International → Daniel K Inouye International SAN–HNL | 1,738 | 301,814 | 87% | 2,614 | Southwest Airlines Co., Alaska Airlines Inc., Hawaiian Airlines Inc., Jet Aviation Flight Services, Inc. | Jan 2025 – Jul 2026 |
| San Diego International → George Bush Intcntl/Houston SAN–IAH | 1,687 | 235,747 | 80% | 1,303 | United Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Minneapolis-St Paul Intl/Wold-Chamberlain SAN–MSP | 1,589 | 241,880 | 81% | 1,532 | Delta Air Lines Inc., Sun Country Airlines d/b/a..., American Airlines Inc., Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Dallas Love Field SAN–DAL | 1,539 | 208,211 | 82% | 1,182 | Southwest Airlines Co., Sun Country Airlines d/b/a... | Jan 2025 – Jul 2026 |
| San Diego International → Newark Liberty International SAN–EWR | 1,510 | 234,135 | 89% | 2,425 | United Air Lines Inc., Alaska Airlines Inc., Federal Express Corporation | Jan 2025 – Jul 2026 |
| San Diego International → Reno/Tahoe International SAN–RNO | 1,465 | 134,306 | 72% | 488 | Southwest Airlines Co., Horizon Air, SkyWest Airlines Inc., Spirit Air Lines +2 | Jan 2025 – Jul 2026 |
| San Diego International → Washington Dulles International SAN–IAD | 1,395 | 213,747 | 86% | 2,253 | United Air Lines Inc., Alaska Airlines Inc., Delta Air Lines Inc., American Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Charlotte/Douglas International SAN–CLT | 1,375 | 216,132 | 83% | 2,077 | American Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Detroit Metro Wayne County SAN–DTW | 1,278 | 189,348 | 78% | 1,956 | Delta Air Lines Inc., Spirit Air Lines, Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Baltimore/Washington International Thurgood Marshall SAN–BWI | 1,143 | 161,573 | 82% | 2,295 | Southwest Airlines Co., Alaska Airlines Inc., Delta Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Boise Air Trml/Gowen Field SAN–BOI | 1,121 | 103,632 | 74% | 749 | Southwest Airlines Co., SkyWest Airlines Inc., Alaska Airlines Inc., Horizon Air | Jan 2025 – Jul 2026 |
| San Diego International → Nashville International SAN–BNA | 1,086 | 143,452 | 78% | 1,751 | Southwest Airlines Co., SkyWest Airlines Inc., Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Orlando International SAN–MCO | 1,083 | 159,595 | 85% | 2,149 | Alaska Airlines Inc., Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Chicago Midway International SAN–MDW | 1,078 | 150,183 | 85% | 1,728 | Southwest Airlines Co., Jet Aviation Flight Services, Inc., Delta Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Charles M Schulz/Sonoma County SAN–STS | 1,051 | 67,944 | 75% | 508 | SkyWest Airlines Inc., Southwest Airlines Co., Horizon Air, Scott Aviation, LLC d/b/a... | Jan 2025 – Jul 2026 |
| San Diego International → Philadelphia International SAN–PHL | 1,025 | 162,648 | 82% | 2,370 | American Airlines Inc., Delta Air Lines Inc., Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → William P Hobby SAN–HOU | 963 | 118,264 | 73% | 1,313 | Southwest Airlines Co., Delta Air Lines Inc., Sun Country Airlines d/b/a... | Jan 2025 – Jul 2026 |
| San Diego International → Kahului SAN–OGG | 857 | 122,281 | 82% | 2,540 | Alaska Airlines Inc., Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Vancouver SAN–YVR international | 741 | 53,968 | 87% | 1,177 | Jazz Aviation LP, Air Canada, Westjet, Sun Country Airlines d/b/a... +2 | Jan 2025 – Jul 2026 |
| San Diego International → San Jose del Cabo SAN–SJD international | 740 | 88,626 | 72% | 802 | Alaska Airlines Inc., Southwest Airlines Co., Air Hamburg... | Jan 2025 – Jul 2026 |
| San Diego International → San Luis Obispo County Regional SAN–SBP | 693 | 38,008 | 72% | 263 | SkyWest Airlines Inc., Horizon Air, Allegiant Air | Jan 2025 – Jul 2026 |
| San Diego International → Albuquerque International Sunport SAN–ABQ | 691 | 68,666 | 66% | 628 | Southwest Airlines Co., Alaska Airlines Inc., American Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Monterey Regional SAN–MRY | 689 | 41,082 | 78% | 375 | SkyWest Airlines Inc., Horizon Air | Jan 2025 – Jul 2026 |
| San Diego International → Tucson International SAN–TUS | 658 | 63,272 | 66% | 367 | Southwest Airlines Co., SkyWest Airlines Inc., American Airlines Inc., Global Crossing Airlines, Inc. +1 | Jan 2025 – Jul 2026 |
| San Diego International → Tampa International SAN–TPA | 641 | 89,353 | 82% | 2,087 | Alaska Airlines Inc., Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Miami International SAN–MIA | 640 | 99,629 | 88% | 2,267 | American Airlines Inc., Delta Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Mahlon Sweet Field SAN–EUG | 634 | 49,264 | 76% | 850 | SkyWest Airlines Inc., Horizon Air, Southwest Airlines Co., Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → San Antonio International SAN–SAT | 617 | 72,257 | 72% | 1,129 | Southwest Airlines Co., American Airlines Inc., Alaska Airlines Inc., Delta Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Tijuana SAN–TIJ international | 615 | 0 | | 18 | Federal Express Corporation, Gulf And Caribbean Cargo | Jan 2025 – Jul 2026 |
| San Diego International → Louisville Muhammad Ali International SAN–SDF | 564 | 170 | 99% | 1,804 | United Parcel Service, American Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Roberts Fld/Redmond Municipal SAN–RDM | 544 | 32,971 | 80% | 823 | Horizon Air, SkyWest Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → London SAN–LHR international | 525 | 118,285 | 88% | 5,485 | British Airways Plc | Jan 2025 – Jul 2026 |
| San Diego International → St. Louis Lambert International SAN–STL | 486 | 66,783 | 83% | 1,557 | Southwest Airlines Co., American Airlines Inc., Alaska Airlines Inc., United Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Indianapolis International SAN–IND | 485 | 37,958 | 82% | 1,782 | Southwest Airlines Co., Federal Express Corporation, Alaska Airlines Inc., United Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Imperial County SAN–IPL | 460 | 0 | | 94 | Federal Express Corporation | Jan 2025 – Jul 2026 |
| San Diego International → Spokane International SAN–GEG | 417 | 53,193 | 75% | 1,027 | Alaska Airlines Inc., Southwest Airlines Co., SkyWest Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Kansas City International SAN–MCI | 396 | 52,388 | 80% | 1,334 | Southwest Airlines Co., Alaska Airlines Inc., Sun Country Airlines d/b/a..., Eastern Air Express, LLC (EAX) +1 | Jan 2025 – Jul 2026 |
| San Diego International → Toronto SAN–YYZ international | 369 | 45,452 | 87% | 2,157 | Air Canada, Air Canada rouge LP, Chartright Air Inc., Scott Aviation, LLC d/b/a... | Jan 2025 – Jul 2026 |
| San Diego International → Rogue Valley Intl/Medford SAN–MFR | 363 | 20,699 | 74% | 734 | Horizon Air, SkyWest Airlines Inc., Allegiant Air | May 2025 – Jul 2026 |
| San Diego International → EL Paso International SAN–ELP | 361 | 34,247 | 63% | 636 | Southwest Airlines Co., Eastern Airlines f/k/a..., Eastern Air Express, LLC (EAX), Air Wisconsin Airlines Corp | Jan 2025 – Jul 2026 |
| San Diego International → Ronald Reagan Washington Ntl SAN–DCA | 358 | 44,387 | 77% | 2,276 | Alaska Airlines Inc., Southwest Airlines Co. | Mar 2025 – Jul 2026 |
| San Diego International → Ellison Onizuka Kona International AT Keahole SAN–KOA | 357 | 53,375 | 87% | 2,556 | Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Seattle Paine Field International SAN–PAE | 351 | 22,847 | 86% | 1,080 | Horizon Air | Jan 2025 – Jul 2026 |
| San Diego International → Louis Armstrong New Orleans International SAN–MSY | 339 | 44,771 | 78% | 1,600 | Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Munich SAN–MUC international | 290 | 68,737 | 86% | 6,025 | Lufthansa German Airlines | Jan 2025 – Jul 2026 |
| San Diego International → Tokyo SAN–NRT international | 282 | 47,458 | 90% | 5,557 | Japan Air Lines Co. Ltd., VistaJet Limited | Jan 2025 – Jul 2026 |
| San Diego International → Lihue SAN–LIH | 279 | 38,090 | 85% | 2,676 | Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Calgary SAN–YYC international | 274 | 35,423 | 86% | 1,279 | Westjet | Jan 2025 – Jul 2026 |
| San Diego International → Frederick W Smith Intl/Memphis SAN–MEM | 262 | 138 | 44% | 1,567 | Federal Express Corporation, Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Raleigh-Durham International SAN–RDU | 208 | 27,895 | 85% | 2,193 | Alaska Airlines Inc., Breeze Aviation Group DBA Breeze, United Air Lines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → General Mitchell International SAN–MKE | 205 | 24,681 | 73% | 1,739 | Southwest Airlines Co., American Airlines Inc., Alaska Airlines Inc., Delta Air Lines Inc. +1 | Apr 2025 – Jul 2026 |
| San Diego International → Puerto Vallarta SAN–PVR international | 200 | 25,917 | 74% | 1,109 | Alaska Airlines Inc., Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Panama City SAN–PTY international | 196 | 26,355 | 81% | 2,911 | Compania Panamena (Copa) | Jun 2025 – Jul 2026 |
| San Diego International → John Glenn Columbus International SAN–CMH | 194 | 24,032 | 74% | 1,964 | Southwest Airlines Co., Air Alsie A/S, Alaska Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Santa Barbara Municipal SAN–SBA | 193 | 6,671 | 46% | 192 | SkyWest Airlines Inc., Horizon Air, Scott Aviation, LLC d/b/a... | Dec 2025 – Jul 2026 |
| San Diego International → Bozeman Yellowstone International SAN–BZN | 181 | 14,722 | 85% | 956 | Horizon Air, SkyWest Airlines Inc., Southwest Airlines Co., Allegiant Air | Jan 2025 – Jul 2026 |
| San Diego International → City Of Colorado Springs Municipal SAN–COS | 170 | 18,660 | 71% | 816 | Southwest Airlines Co., Jet Aviation Flight Services, Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Fort Lauderdale/Hollywood International SAN–FLL | 170 | 24,847 | 84% | 2,269 | Alaska Airlines Inc. | Jan 2025 – May 2026 |
| San Diego International → Tulsa International SAN–TUL | 142 | 8,657 | 77% | 1,237 | Horizon Air, American Airlines Inc., ADVANCED AIR, LLC, Southwest Airlines Co. | Aug 2025 – Jul 2026 |
| San Diego International → Norfolk International SAN–ORF | 141 | 16,803 | 87% | 2,330 | Breeze Aviation Group DBA Breeze, Alaska Airlines Inc., Southwest Airlines Co. | Jan 2025 – Jul 2026 |
| San Diego International → Montreal SAN–YUL international | 117 | 13,070 | 82% | 2,460 | Air Canada | May 2025 – Jul 2026 |
| San Diego International → San Diego International SAN–SAN | 115 | 0 | 0% | 0 | SkyWest Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Amsterdam SAN–AMS international | 101 | 24,426 | 84% | 5,613 | Klm Royal Dutch Airlines | May 2025 – Jul 2026 |
| San Diego International → Ontario International SAN–ONT | 90 | 1,875 | 74% | 94 | Federal Express Corporation, Alaska Airlines Inc., United Parcel Service, Delta Air Lines Inc. +3 | Jan 2025 – Jul 2026 |
| San Diego International → Jackson Hole SAN–JAC | 89 | 3,665 | 54% | 828 | SkyWest Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Eppley Airfield SAN–OMA | 80 | 11,075 | 81% | 1,313 | Southwest Airlines Co., American Airlines Inc., United Air Lines Inc., Alaska Airlines Inc. | Aug 2025 – Jul 2026 |
| San Diego International → Pittsburgh International SAN–PIT | 75 | 9,503 | 81% | 2,106 | Southwest Airlines Co., Breeze Aviation Group DBA Breeze, Alaska Airlines Inc., American Airlines Inc. +1 | Jan 2025 – Jul 2026 |
| San Diego International → Cincinnati/Northern Kentucky International SAN–CVG | 54 | 6,399 | 91% | 1,865 | Breeze Aviation Group DBA Breeze, Federal Express Corporation, Delta Air Lines Inc. | May 2025 – Jul 2026 |
| San Diego International → Yampa Valley SAN–HDN | 50 | 2,269 | 60% | 769 | SkyWest Airlines Inc. | Jan 2025 – Mar 2026 |
| San Diego International → Kalispell SAN–FCA | 48 | 3,034 | 83% | 1,086 | Horizon Air, SkyWest Airlines Inc. | Jun 2025 – Jul 2026 |
| San Diego International → Eagle County Regional SAN–EGE | 46 | 1,338 | 38% | 745 | SkyWest Airlines Inc. | Jan 2025 – Mar 2026 |
| San Diego International → Tapachula SAN–TAP international | 43 | 2,440 | 37% | 1,989 | Global Crossing Airlines, Inc. | May 2025 – Jul 2026 |
| San Diego International → Friedman Memorial SAN–SUN | 39 | 1,440 | 49% | 759 | Horizon Air | Dec 2025 – Mar 2026 |
| San Diego International → Jacksonville International SAN–JAX | 34 | 4,061 | 87% | 2,088 | Breeze Aviation Group DBA Breeze | Apr 2025 – Jul 2026 |
| San Diego International → Ted Stevens Anchorage International SAN–ANC | 25 | 3,635 | 86% | 2,452 | Alaska Airlines Inc. | May 2025 – Jul 2026 |
| San Diego International → Missoula Montana SAN–MSO | 25 | 1,641 | 86% | 992 | Horizon Air, SkyWest Airlines Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Villahermosa SAN–VSA international | 20 | 2,193 | 77% | 1,823 | Global Crossing Airlines, Inc., Eastern Air Express, LLC (EAX) | May 2025 – Jul 2026 |
| San Diego International → Provo Municipal SAN–PVU | 12 | 1,745 | 87% | 599 | Allegiant Air, Global Crossing Airlines, Inc., Breeze Aviation Group DBA Breeze | Jan 2025 – Dec 2025 |
| San Diego International → Valley International SAN–HRL | 11 | 431 | 35% | 1,257 | Global Crossing Airlines, Inc., Southwest Airlines Co. | Jan 2025 – Feb 2026 |
| San Diego International → Palm Springs International SAN–PSP | 10 | 164 | 17% | 85 | SkyWest Airlines Inc., American Airlines Inc., Alaska Airlines Inc. | Feb 2025 – Jun 2026 |
| San Diego International → Des Moines International SAN–DSM | 9 | 1,328 | 81% | 1,428 | Allegiant Air, United Air Lines Inc. | May 2025 – Jul 2026 |
| San Diego International → Long Beach (Daugherty Field) SAN–LGB | 9 | 1,153 | 72% | 93 | Southwest Airlines Co., Delta Air Lines Inc., Sun Country Airlines d/b/a... | Jan 2025 – May 2026 |
| San Diego International → Phoenix SAN–AZA | 8 | 55 | 4% | 324 | Global Crossing Airlines, Inc., Eastern Air Express, LLC (EAX), Eastern Airlines f/k/a..., Air Wisconsin Airlines Corp | Jan 2025 – Jul 2026 |
| San Diego International → Okc Will Rogers International SAN–OKC | 6 | 907 | 85% | 1,137 | American Airlines Inc., Southwest Airlines Co. | Mar 2025 – Apr 2026 |
| San Diego International → Wichita Dwight D Eisenhower Ntl SAN–ICT | 5 | 625 | 70% | 1,166 | American Airlines Inc., Southwest Airlines Co., United Air Lines Inc. | Nov 2025 – Jul 2026 |
| San Diego International → Albany International SAN–ALB | 4 | 591 | 87% | 2,445 | United Air Lines Inc., Alaska Airlines Inc., JetBlue Airways | Sep 2025 – Jul 2026 |
| San Diego International → Bellingham International SAN–BLI | 4 | 616 | 99% | 1,142 | Allegiant Air | May 2025 – Aug 2025 |
| San Diego International → Hollywood Burbank SAN–BUR | 4 | 136 | 37% | 122 | SkyWest Airlines Inc., Delta Air Lines Inc., Southwest Airlines Co. | Feb 2025 – Feb 2026 |
| San Diego International → Dane County Rgnl/Truax Field SAN–MSN | 4 | 455 | 70% | 1,672 | United Air Lines Inc., Global Crossing Airlines, Inc. | Jul 2025 – Jun 2026 |
| San Diego International → Chicago/Rockford International SAN–RFD | 4 | 608 | 84% | 1,667 | United Air Lines Inc., American Airlines Inc., Alaska Airlines Inc. | Aug 2025 – May 2026 |
| San Diego International → Van Nuys SAN–VNY | 4 | 12 | 57% | 126 | Scott Aviation, LLC d/b/a..., Jet Story | Sep 2025 – Jul 2026 |
| San Diego International → Rick Husband Amarillo International SAN–AMA | 3 | 495 | 86% | 905 | American Airlines Inc. | Jun 2025 – Jul 2026 |
| San Diego International → Boeing Fld/King County International SAN–BFI | 3 | 113 | 25% | 1,056 | Sun Country Airlines d/b/a..., Delta Air Lines Inc. | Apr 2026 – May 2026 |
| San Diego International → Birmingham-Shuttlesworth International SAN–BHM | 3 | 487 | 88% | 1,759 | Delta Air Lines Inc., Southwest Airlines Co. | May 2025 – Jun 2026 |
| San Diego International → The Eastern Iowa SAN–CID | 3 | 553 | 94% | 1,531 | United Air Lines Inc., American Airlines Inc. | Aug 2025 – Jun 2026 |
| San Diego International → Laughlin/Bullhead International SAN–IFP | 3 | 98 | 18% | 225 | Sun Country Airlines d/b/a... | Jan 2025 – May 2026 |
| San Diego International → Richmond International SAN–RIC | 3 | 269 | 49% | 2,265 | United Air Lines Inc., Delta Air Lines Inc. | May 2026 – Jul 2026 |
| San Diego International → Scottsbluff/Western Nebraska Rgnl/Wm B Heilig Field SAN–BFF | 2 | 390 | 98% | 977 | United Air Lines Inc. | Aug 2025 – Jun 2026 |
| San Diego International → Paris SAN–CDG international | 2 | 550 | 94% | 5,698 | Compagnie Natl Air France | Apr 2026 – Apr 2026 |
| San Diego International → Northern Colorado Regional SAN–FNL | 2 | 0 | 0% | 860 | Alaska Airlines Inc. | Oct 2025 – Nov 2025 |
| San Diego International → Westchester County SAN–HPN | 2 | 135 | 84% | 2,449 | Jet Aviation Flight Services, Inc., TEM Enterprises dba Avelo Airlines | Mar 2026 – Jul 2026 |
| San Diego International → London SAN–LTN international | 2 | 7 | 27% | 5,470 | AVCON JET MALTA LTD, VistaJet Limited | Sep 2025 – Nov 2025 |
| San Diego International → Mexico City SAN–NLU international | 2 | 92 | 25% | 1,436 | Sun Country Airlines d/b/a... | Sep 2025 – Feb 2026 |
| San Diego International → Rhode Island TF Green International SAN–PVD | 2 | 255 | 75% | 2,567 | JetBlue Airways, Allegiant Air | Aug 2025 – Nov 2025 |
| San Diego International → Southwest Florida International SAN–RSW | 2 | 0 | 0% | 2,164 | Southwest Airlines Co. | Jul 2026 – Jul 2026 |
| San Diego International → Addison SAN–ADS | 1 | 2 | 22% | 1,182 | Jet Aviation Flight Services, Inc. | Sep 2025 – Sep 2025 |
| San Diego International → Alexandria International SAN–AEX | 1 | 0 | 0% | 1,447 | Global Crossing Airlines, Inc. | Jan 2025 – Mar 2026 |
| San Diego International → Malaga SAN–AGP international | 1 | 1 | 7% | 5,983 | FAI rent-a-jet AG | Jul 2025 – Mar 2026 |
| San Diego International → Augusta Regional AT Bush Field SAN–AGS | 1 | 187 | 99% | 2,035 | Delta Air Lines Inc. | May 2025 – Aug 2025 |
| San Diego International → Waterloo Regional SAN–ALO | 1 | 136 | 76% | 1,511 | Allegiant Air | Mar 2026 – Mar 2026 |
| San Diego International → Centennial SAN–APA | 1 | 16 | 100% | 834 | CFM Inc d/b/a Contour... | Jun 2026 – Jun 2026 |
| San Diego International → Bradley International SAN–BDL | 1 | 154 | 96% | 2,502 | JetBlue Airways | Jul 2026 – Jul 2026 |
| San Diego International → Laurence G Hanscom Field SAN–BED | 1 | 12 | 92% | 2,573 | Jet Aviation Flight Services, Inc. | Apr 2025 – Feb 2026 |
| San Diego International → Meadows Field SAN–BFL | 1 | 0 | 0% | 215 | Scott Aviation, LLC d/b/a... | Aug 2025 – Aug 2025 |
| San Diego International → Berne SAN–BRN international | 1 | 2 | 18% | 5,963 | Volkswagen AirSevice GmbH... | Aug 2025 – Aug 2025 |
| San Diego International → Buffalo Niagara International SAN–BUF | 1 | 136 | 86% | 2,196 | JetBlue Airways | Jun 2025 – Sep 2025 |
| San Diego International → Southern Cross SAN–C01 | 1 | 1 | 12% | 150 | Scott Aviation, LLC d/b/a... | Oct 2025 – Oct 2025 |
| San Diego International → Lovell Field SAN–CHA | 1 | 197 | 99% | 1,838 | Delta Air Lines Inc. | Jun 2025 – Mar 2026 |
| San Diego International → Charleston Afb/Intl SAN–CHS | 1 | 112 | 82% | 2,150 | Breeze Aviation Group DBA Breeze | Jul 2025 – May 2026 |
| San Diego International → Carlsbad SAN–CLD | 1 | 2 | 29% | 28 | ADVANCED AIR, LLC | Dec 2025 – Dec 2025 |
| San Diego International → Cleveland-Hopkins International SAN–CLE | 1 | 132 | 83% | 2,026 | JetBlue Airways | Apr 2025 – Jun 2026 |
| San Diego International → St. Louis Downtown SAN–CPS | 1 | 57 | 31% | 1,567 | Sun Country Airlines d/b/a... | Mar 2026 – Mar 2026 |
| San Diego International → Corpus Christi International SAN–CRP | 1 | 144 | 87% | 1,224 | United Air Lines Inc. | Jun 2025 – Mar 2026 |
| San Diego International → Dubois Municipal SAN–DUB international | 1 | 8 | 57% | 5,209 | VistaJet Limited | Dec 2025 – Dec 2025 |
| San Diego International → Northwest Florida Beaches International SAN–ECP | 1 | 0 | 0% | 1,853 | Concierge U Ltd. d/b/a Jet... | Jul 2026 – Jul 2026 |
| San Diego International → Edinburgh SAN–EDI international | 1 | 2 | 15% | 5,198 | Air Alsie A/S | Oct 2025 – Oct 2025 |
| San Diego International → Topeka Regional SAN–FOE | 1 | 128 | 69% | 1,278 | Sun Country Airlines d/b/a... | Mar 2026 – Mar 2026 |
| San Diego International → Francis S Gabreski SAN–FOK | 1 | 9 | 69% | 2,506 | CFM Inc d/b/a Contour... | Jul 2026 – Jul 2026 |
| San Diego International → Fort Worth Meacham International SAN–FTW | 1 | 100 | 64% | 1,153 | Allegiant Air | Mar 2026 – Mar 2026 |
| San Diego International → Claremore Regional SAN–GCM international | 1 | 6 | 43% | 2,398 | VistaJet Limited | Mar 2026 – Mar 2026 |
| San Diego International → Guadalajara SAN–GDL international | 1 | 57 | 20% | 1,199 | Aerovias Nacl De Colombia | Jun 2026 – Jun 2026 |
| San Diego International → Robert Gray Army Airfield SAN–GRK | 1 | 0 | 0% | 1,142 | Air Wisconsin Airlines Corp | Jul 2026 – Jul 2026 |
| San Diego International → Piedmont Triad International SAN–GSO | 1 | 119 | 87% | 2,127 | Breeze Aviation Group DBA Breeze | Jul 2026 – Jul 2026 |
| San Diego International → Henderson Executive SAN–HND international | 1 | 11 | 79% | 5,594 | VistaJet Limited | Jul 2026 – Jul 2026 |
| San Diego International → Huntsville Intl-Carl T Jones Field SAN–HSV | 1 | 191 | 100% | 1,751 | Delta Air Lines Inc. | Jul 2025 – Aug 2025 |
| San Diego International → Idaho Falls Regional SAN–IDA | 1 | 3 | 27% | 795 | Jet Aviation Flight Services, Inc. | Jan 2025 – Jul 2026 |
| San Diego International → Long Island Mac Arthur SAN–ISP | 1 | 108 | 60% | 2,481 | Allegiant Air | Aug 2025 – Aug 2025 |
| San Diego International → Laramie Regional SAN–LAR | 1 | 150 | 83% | 868 | Allegiant Air | Nov 2025 – Nov 2025 |
| San Diego International → Lubbock Preston Smith International SAN–LBB | 1 | 120 | 88% | 892 | Southwest Airlines Co. | May 2026 – May 2026 |
| San Diego International → Lafayette Rgnl/Paul Fournet Field SAN–LFT | 1 | 146 | 88% | 1,495 | United Air Lines Inc. | Feb 2026 – Feb 2026 |
| San Diego International → Bill And Hillary Clinton Ntl/Adams Field SAN–LIT | 1 | 155 | 89% | 1,441 | Southwest Airlines Co. | Apr 2025 – Mar 2026 |
| San Diego International → Loreto SAN–LTO international | 1 | 176 | 99% | 583 | Alaska Airlines Inc. | Apr 2026 – Apr 2026 |
| San Diego International → Cincinnati Muni/Lunken Field SAN–LUK | 1 | 49 | 26% | 1,879 | Sun Country Airlines d/b/a... | May 2026 – May 2026 |
| San Diego International → Lewiston/Nez Perce County SAN–LWS | 1 | 150 | 94% | 941 | Alaska Airlines Inc. | Sep 2025 – Sep 2025 |
| San Diego International → Madrid SAN–MAD international | 1 | 10 | 71% | 5,856 | VistaJet Limited | Jun 2026 – Jun 2026 |
| San Diego International → Midland International Air And Space Port SAN–MAF | 1 | 70 | 40% | 878 | Southwest Airlines Co. | Jan 2025 – Jun 2026 |
| San Diego International → Harrisburg International SAN–MDT | 1 | 170 | 88% | 2,289 | Delta Air Lines Inc. | Oct 2025 – Oct 2025 |
| San Diego International → Quad Cities International SAN–MLI | 1 | 150 | 75% | 1,584 | United Air Lines Inc. | Jul 2026 – Jul 2026 |
| San Diego International → Smyrna SAN–MQY | 1 | 2 | 12% | 1,760 | CFM Inc d/b/a Contour... | May 2025 – Mar 2026 |
| San Diego International → Mazatlan SAN–MZT international | 1 | 52 | 28% | 937 | Sun Country Airlines d/b/a... | Aug 2025 – Aug 2025 |
| San Diego International → Nice SAN–NCE international | 1 | 5 | 36% | 6,116 | VistaJet Limited | Jun 2025 – Jun 2026 |
| San Diego International → Ogden-Hinckley SAN–OGD | 1 | 140 | 75% | 650 | Sun Country Airlines d/b/a... | Mar 2026 – Mar 2026 |
| San Diego International → Miami-Opa Locka Executive SAN–OPF | 1 | 23 | 15% | 2,265 | Global Crossing Airlines, Inc. | Sep 2025 – Sep 2025 |
| San Diego International → West Palm Beach/Palm Beach SAN–PBI | 1 | 167 | 97% | 2,257 | American Airlines Inc. | Feb 2026 – Feb 2026 |
| San Diego International → Beijing SAN–PEK international | 1 | 1 | 7% | 6,360 | VistaJet Limited | Mar 2026 – Mar 2026 |
| San Diego International → Rapid City Regional SAN–RAP | 1 | 189 | 94% | 1,091 | United Air Lines Inc. | Jul 2026 – Jul 2026 |
| San Diego International → Rifle Garfield County SAN–RIL | 1 | 23 | 77% | 706 | CFM Inc d/b/a Contour... | Dec 2025 – Dec 2025 |
| San Diego International → Orlando Sanford International SAN–SFB | 1 | 107 | 59% | 2,146 | Allegiant Air | Nov 2025 – Nov 2025 |
| San Diego International → St. George Regional SAN–SGU | 1 | 0 | 0% | 363 | SkyWest Airlines Inc. | Feb 2026 – Feb 2026 |
| San Diego International → San Jose SAN–SJO international | 1 | 44 | 25% | 2,619 | Global Crossing Airlines, Inc. | Feb 2025 – Apr 2026 |
| San Diego International → Luis Munoz Marin International SAN–SJU | 1 | 0 | 0% | 3,310 | Delta Air Lines Inc. | Jan 2026 – Jan 2026 |
| San Diego International → Sarasota/Bradenton International SAN–SRQ | 1 | 166 | 95% | 2,098 | Southwest Airlines Co. | Feb 2026 – Feb 2026 |
| San Diego International → New York Stewart International SAN–SWF | 1 | 96 | 62% | 2,428 | Allegiant Air | Oct 2025 – Oct 2025 |
| San Diego International → Syracuse Hancock International SAN–SYR | 1 | 163 | 91% | 2,330 | United Air Lines Inc. | Jan 2025 – Sep 2025 |
| San Diego International → Teterboro SAN–TEB | 1 | 1 | 12% | 2,431 | Scott Aviation, LLC d/b/a... | Nov 2025 – Nov 2025 |
| San Diego International → Eugene F Kranz Toledo Express SAN–TOL | 1 | 142 | 73% | 1,927 | Delta Air Lines Inc. | Jan 2026 – Jan 2026 |
| San Diego International → Tulum SAN–TQO international | 1 | 0 | 0% | 2,014 | Global Crossing Airlines, Inc. | May 2026 – May 2026 |
| San Diego International → Trenton Mercer SAN–TTN | 1 | 117 | 63% | 2,392 | Allegiant Air | Sep 2025 – Sep 2025 |
| San Diego International → Warsaw SAN–WAW international | 1 | 2 | 15% | 6,064 | Jet Story | Dec 2025 – Dec 2025 |
| San Diego International → Winnipeg SAN–YWG international | 1 | 37 | 53% | 1,565 | Air Canada | Dec 2025 – Dec 2025 |
| San Diego International → Zurich SAN–ZRH international | 1 | 3 | 21% | 5,970 | VistaJet Limited | Mar 2025 – Mar 2026 |