| 1 | AEE | Aegean Airlines, S.A. | IATA: A3, Callsign: Aegean, IATA Prefix: 390, Name changed from Aegean Aviation S.A. Merger with Cronus Airlines X5/CUS | GR | AVCODES |
| 2 | AEE | Air Europe Express | IATA: AX, Callsign: Euroexpress, Formerly Connectair | GB | AVCODES |
| 3 | AEE | Aegean Aviation, S.A. | IATA: A3, Callsign: Aegean, IATA Prefix: 390, Name changed to Aegean Airlines S.A. Founded in 1987. | GR | AVCODES |
| 4 | AEE | Aegean Airlines | IATA: A3 | | ICAO1 |
| 5 | AEE | Aegean Airlines | | GR | TRAFFIC |
| 6 | AEEC | ALPINE EXPRESS CORP | | | SCAC3 |
| 7 | AEEC | ADVANTAGE EXPRESS INC | | | SCAC4 |
| 8 | AEEC | Aviación del Ejército Ecuatoriano | Real: AEE, The flying component of the Ecuadorian Army, specializing in supporting land forces, transport, and, since 1996, functioning as a full, independent arm within the army. | EC | TRAFFIC |
| 9 | AEED | ALEET EXPEDITING | | | SCAC4 |
| 10 | AEEN | A & A TRANSPORTATION RESOURCES INC | | | SCAC4 |
| 11 | AEEP | AMERICAN EAGLE EXPRESS INC | | | SCAC3 |
| 12 | AEEP | AMERICAN EAGLE EXPRESS INC | | | SCAC4 |
| 13 | AEES | AERONAUTICS EXPRESS OF ILLINOIS INC | | | SCAC3 |
| 14 | AEEU | Alion Energy | | | RSRV |
