| San Diego, CA → San Francisco, CA (Metropolitan Area) | 5379 | $186 | Southwest |
| New York City, NY (Metropolitan Area) → San Diego, CA | 2431 | $334 | United |
| Denver, CO → San Diego, CA | 2078 | $169 | Southwest |
| Sacramento, CA → San Diego, CA | 2023 | $167 | Southwest |
| San Diego, CA → Seattle, WA | 1968 | $214 | Alaska |
| Chicago, IL → San Diego, CA | 1954 | $226 | United |
| Las Vegas, NV → San Diego, CA | 1863 | $145 | Southwest |
| San Diego, CA → Washington, DC (Metropolitan Area) | 1694 | $328 | United |
| Phoenix, AZ → San Diego, CA | 1671 | $162 | Southwest |
| Dallas/Fort Worth, TX → San Diego, CA | 1636 | $255 | American |
| Salt Lake City, UT → San Diego, CA | 1269 | $201 | Delta |
| Boston, MA (Metropolitan Area) → San Diego, CA | 1168 | $320 | JetBlue |
| Portland, OR → San Diego, CA | 1069 | $215 | Alaska |
| Austin, TX → San Diego, CA | 956 | $225 | Southwest |
| Miami, FL (Metropolitan Area) → San Diego, CA | 902 | $341 | American |
| Minneapolis/St. Paul, MN → San Diego, CA | 901 | $317 | Delta |
| Orlando, FL → San Diego, CA | 880 | $288 | Alaska |
| Houston, TX → San Diego, CA | 814 | $343 | United |
| Atlanta, GA (Metropolitan Area) → San Diego, CA | 791 | $391 | Delta |
| Philadelphia, PA → San Diego, CA | 600 | $371 | American |
| Reno, NV → San Diego, CA | 528 | $194 | Southwest |
| San Diego, CA → Tampa, FL (Metropolitan Area) | 519 | $270 | Alaska |
| Detroit, MI → San Diego, CA | 499 | $427 | Delta |
| Nashville, TN → San Diego, CA | 494 | $311 | Southwest |
| Boise, ID → San Diego, CA | 442 | $186 | Alaska |
| Kansas City, MO → San Diego, CA | 389 | $278 | Southwest |
| Charlotte, NC → San Diego, CA | 374 | $384 | American |
| San Diego, CA → Spokane, WA | 348 | $186 | Alaska |
| San Antonio, TX → San Diego, CA | 345 | $290 | Southwest |
| San Diego, CA → St. Louis, MO | 343 | $305 | Southwest |
| Fresno, CA → San Diego, CA | 328 | $158 | Alaska |
| Raleigh/Durham, NC → San Diego, CA | 314 | $329 | American |
| Indianapolis, IN → San Diego, CA | 309 | $289 | Southwest |
| New Orleans, LA → San Diego, CA | 297 | $297 | Southwest |
| Norfolk, VA (Metropolitan Area) → San Diego, CA | 264 | $353 | American |
| Columbus, OH → San Diego, CA | 259 | $271 | Southwest |
| Albuquerque, NM → San Diego, CA | 252 | $246 | Southwest |