This is a list of airlines which have an air operator's certificate issued by the Federal Aviation Administration of the United States.
Note:Destinations in bold indicate primary hubs, those in italic indicate secondary hubs, while those with regular font indicate focus cities.
| Airline | Image | IATA | ICAO | Callsign | Hubs and focus cities | Founded | Notes |
|---|---|---|---|---|---|---|---|
| Air Flamenco |  | F4 | WAF | FLAMENCO | San Juan (International) Ceiba Culebra San Juan (Isla Grande) Vieques | 1976 | |
| Borinquen Air |  | FD; 3B | BNA | San Juan (International) | 1960 | ||
| Culebra Air Services | Culebra San Juan (International) | 1998 | |||||
| M&N Aviation |  | San Juan (International) | 1992 | ||||
| Merlin Express |  | MEI | MERIN EXPRESS | Aguadilla Santiago de los Caballeros Providenciales | |||
| Prams Air |  | 2005 | |||||
| Pro-Air Services | San Juan (International) | 1981 | |||||
| San Juan Aviation | JI | San Juan (International) | |||||
| Seaborne Airlines |  | BB | SBS | SEABORNE | San Juan (International) St. Croix St. Thomas | 1992 | |
| Vieques Air Link |  | V4 | VES | VIEQUES | Vieques | 1965 |