| 1 | SJO to ZRH Zurich, Switzerland | 5,838 mi | 12h 38m | Edelweiss Air | weekly |
| 2 | SJO to FRA Frankfurt, Germany | 5,811 mi | 12h 34m | Lufthansa | 3×/wk |
| 3 | SJO to AMS Amsterdam, Netherlands | 5,630 mi | 12h 12m | KLM | 3×/wk |
| 4 | SJO to CDG Paris, France | 5,552 mi | 12h 2m | Air France | 1/day |
| 5 | SJO to MAD Madrid, Spain | 5,281 mi | 11h 29m | Iberia and Evelop | 1-2/day |
| 6 | SJO to SFO San Francisco, United States | 3,041 mi | 6h 51m | United Airlines | 1/day |
| 7 | SJO to LAX Los Angeles, United States | 2,723 mi | 6h 12m | Alaska Airlines and United Airlines | 1-2/day |
| 8 | SJO to YUL Montreal, Canada | 2,529 mi | 5h 48m | Air Canada and Air Transat | 3×/wk |
| 9 | SJO to DEN Denver, United States | 2,416 mi | 5h 34m | United Airlines and Southwest Airlines | 3×/wk |
| 10 | SJO to YYZ Toronto, Canada | 2,343 mi | 5h 25m | Air Canada | 1/day |
| 11 | SJO to ORD Chicago, United States | 2,221 mi | 5h 10m | United Airlines | weekly |
| 12 | SJO to JFK New York, United States | 2,211 mi | 5h 9m | JetBlue Airways | 1/day |
| 13 | SJO to EWR Newark, United States | 2,208 mi | 5h 8m | United Airlines | 1/day |
| 14 | SJO to BWI Baltimore, United States | 2,069 mi | 4h 51m | Southwest Airlines | 2×/wk |
| 15 | SJO to DFW Dallas, United States | 1,781 mi | 4h 15m | American Airlines | 1/day |
| 16 | SJO to CLT Charlotte, United States | 1,755 mi | 4h 12m | American Airlines | 1/day |
| 17 | SJO to ATL Atlanta, United States | 1,634 mi | 3h 57m | Delta Air Lines | 1-2/day |
| 18 | SJO to IAH Houston, United States | 1,556 mi | 3h 48m | United Airlines | 4-5/day |
| 19 | SJO to HOU Houston, United States | 1,534 mi | 3h 45m | Southwest Airlines | 1-2/day |
| 20 | SJO to MTY Monterrey, Mexico | 1,507 mi | 3h 42m | VivaAerobus | 2×/wk |
| 21 | SJO to GDL Guadalajara, Mexico | 1,464 mi | 3h 36m | Volaris Costa Rica | 2×/wk |
| 22 | SJO to MCO Orlando, United States | 1,288 mi | 3h 14m | Southwest Airlines, Volaris Costa Rica, and JetBlue Airways | 3-4/day |
| 23 | SJO to MEX Mexico City, Mexico | 1,187 mi | 3h 2m | Aeromexico and Avianca | 3/day |
| 24 | SJO to FLL Fort Lauderdale, United States | 1,142 mi | 2h 56m | JetBlue Airways | 1/day |
| 25 | SJO to SDQ Santo Domingo, Dominican Republic | 1,134 mi | 2h 55m | Arajet | 2×/wk |