| 1 | EE | Aero Airlines A.S. | ICAO: EAY, Callsign: Reval, IATA Prefix: 350, Founded in 2000. Commenced operations in 2002. Ceased operations in January 2008. Setup by Finnair | EST | AVCODES |
| 2 | EE | Euroberlin | ICAO: EEB, Callsign: Eurober, Ceased operations. Formed by Air France and Lufthansa | F | AVCODES |
| 3 | EE | Goldwing Airlines S.p.A. | ICAO: GDW, Ceased operations during March 2001. Designator EE recalled by IATA. Founded in December 2000. | I | AVCODES |
| 4 | EE | Executair (Nigeria) Ltd. | Callsign: Executair, | WAN | AVCODES |
| 5 | EE | Eurofly Company | Callsign: Eurofly, | I | AVCODES |
| 6 | EE | Eastern Skyjets | ICAO: ESJ, Callsign: Eastern Skyjets, Designator EE recalled by IATA. IATA Designator changed from EA*. | UAE | AVCODES |
| 7 | EE | Eastern Air Lines Group, Inc. | ICAO: EAL, Callsign: Eastern, IATA designator changed to EA | USA | AVCODES |
| 8 | EE | Regional Jet Ou | ICAO: EST, Callsign: Reval, Nmae changed to Regional Jet Ou d/b/a Xfly. Subsidary of Nordic Aviation Group. | EST | AVCODES |
| 9 | EE | Regional Jet Ou d/b/a Xfly | ICAO: EST, Callsign: Reval, Name changed from Regional Jet Ou. Subsidary of Nordic Aviation Group. | EST | AVCODES |
| 10 | EE | Ellis & Eastern Co. | added 10/1996; 7/2000-7/2005 | | NAKINA |
| 11 | EE | Ellis & Eastern Co. | added 10/96; 7/2000 | | NRHS |
| 12 | EE | ELLIS & EASTERN CO. | | | PWRC |
| 13 | EE | Ellis and Eastern | | | RSRV |
| 14 | EE | ELLIS & EASTERN COMPANY | | | SCAC4 |
| 15 | EE | Edelaraudtee | | EE | VKM |
| 16 | EEA | Ecuatoriana de Aviacion, S.A. | IATA: EU, Callsign: Ecuatoriana, IATA Prefix: 341, | EC | AVCODES |
| 17 | EEA | Empresa Ecuatoriana De Aviacion | IATA: EU | | ICAO1 |
| 18 | EEA | Euregio Eisenbahn Ahaus-Alstätte e.V. | Alstätte | D | privat-bahn.de |
| 19 | EEA | EUREGIO EISENBAH Ahaus-Alstätte | | DE | VKM |
| 20 | EEAA | EAST EXPRESS INC | | | SCAC4 |
| 21 | EEAF | Estonian Air Force (Eesti Ohuvägi) | | EST | TRAFFIC |
| 22 | EEAT | ENTERPRISE EXPRESS & TRUCKMEN INC | | | SCAC3 |
| 23 | EEAT | EAGLE MACHINE INC | | | SCAC4 |
| 24 | EEB | Euroberlin | IATA: EE, Callsign: Eurober, Ceased operations. Formed by Air France and Lufthansa | F | AVCODES |
| 25 | EEB | Emsländische Eisenbahn GmbH | Meppen | D | privat-bahn.de |
| 26 | EEB | Emsländische Eisenbahnen | | D | TRAFFIC |
| 27 | EEB | Emsländische Eisenbahn | | DE | VKM |
| 28 | EEBF | EDDY, E B FOREST PRODUCTS LTD | | | SCAC3 |
| 29 | EEBF | ESTAD ESTATES INC | | | SCAC4 |
| 30 | EEBK | EAGLE BEAK | | | SCAC3 |
| 31 | EEC | Carry Air | Callsign: Quick Speed, | F | AVCODES |
| 32 | EEC | East Erie Commercial R.R. | 7/1923-7/2005 | | NAKINA |
| 33 | EEC | East Erie Commercial R.R. | 4/38-7/2000 | | NRHS |
| 34 | EEC | EAST ERIE COMMERCIAL RAILROAD | | | PWRC |
| 35 | EEC | East Erie Commercial Railroad | | | RSRV |
| 36 | EEC | EAST ERIE COMMERCIAL RAILROAD | | | SCAC4 |
| 37 | EEC | East Erie Commercial R.R. | | USA | TRAFFIC |
| 38 | EECL | EXPRESS FREIGHT SYSTEMS INCORPORATE | | | SCAC4 |
| 39 | EECM | ENVIROSCA | | | SCAC4 |
| 40 | EECO | ENCORE EXPRESS COMPANY INC | | | SCAC3 |
| 41 | EECO | EXPRESSO AMERICA INC | | | SCAC4 |
| 42 | EECU | FUJIAN ELEGANT CREATION ELECTRONIC CHEMICAL CORP | | PRC | BIC |
| 43 | EECW | Europa Express City | Real: EEC | PL | TRAFFIC |
| 44 | EEDA | EED | | | SCAC4 |
| 45 | EEDJ | ENNS, EDWIN J | | | SCAC4 |
| 46 | EEDM | EDGE EDM TECHNOLOGIES INC | | | SCAC4 |
| 47 | EEDR | EXPORT EXPEDITORS LLC | | | SCAC4 |
| 48 | EEDS | EMPIRE EXPRESS DELIVERY SERVICE INC | | | SCAC4 |
| 49 | EEE | European Regions Airlines | IATA: EA, Declared bankrupt on 10 October 2000. | E | AVCODES |
| 50 | EEEE | EIGHT EIGHT EIGHT (888) EXPRESS | | | SCAC3 |
| 51 | EEEI | EAST END EXPEDITING INC | | | SCAC4 |
| 52 | EEEL | ECKERT & ECKERT ENTERPRISES LLC | | | SCAC4 |
| 53 | EEEM | ESPECIA | | | SCAC4 |
| 54 | EEEP | EAGLE EYE EXPRESS | | | SCAC4 |
| 55 | EEF | Ema Air, S.A. | Callsign: Melissa, | PA | AVCODES |
| 56 | EEF | Estonian Airforce | Callsign: Estonian Airforce, | EST | AVCODES |
| 57 | EEFG | EIGTH EIGHT (88) FREIGHT | | | SCAC4 |
| 58 | EEFT | E EIGHTY FIVE (85) TRANSPORT LLC | | | SCAC4 |
| 59 | EEGA | ELLIOTT, G PATRICK | | | SCAC4 |
| 60 | EEI | Elisystem Eliagricola Srl | Callsign: Elisystem, Name changed from Elisystem | I | AVCODES |
| 61 | EEI | Elisystem | Callsign: Elisystem, Name changed to Elisystem Eliagricola Srl | I | AVCODES |
| 62 | EEIA | EPIC ENTERPRISES INC | | | SCAC4 |
| 63 | EEIB | EXPEDITED-EXPRE | | | SCAC4 |
| 64 | EEIF | EASY EFFORT INNOVATIVE FITNESS PROD | | | SCAC4 |
| 65 | EEIH | ESSEX | | | SCAC4 |
| 66 | EEIM | EEI MOVERS INC | | | SCAC4 |
| 67 | EEIO | EEI MOBILE | | | SCAC4 |
| 68 | EEIQ | EDELMAN ENTERPRISES INC | | | SCAC4 |
| 69 | EEIR | EURO EXPRESS INC | | | SCAC4 |
| 70 | EEIS | ELIJAHS ENTERPRISES INC | | | SCAC4 |
| 71 | EEIX | Electric Energy, Inc. | 1/1994-7/2005 (not listed) | | NAKINA |
| 72 | EEIX | Electronic Energy, Inc. | Jan-94 | | NRHS |
| 73 | EEIX | Electric Energy, Inc. | Jul-00 | | NRHS |
| 74 | EEIX | ELECTRIC ENERGY, INC. | | | PWRC |
| 75 | EEIX | Electric Energy | | | RSRV |
| 76 | EEIX | ELECTRIC ENERGY, INC. | | | SCAC4 |
| 77 | EEJ | Euro Executive Jet Ltd. | Callsign: Ejay, | GB | AVCODES |
| 78 | EEJA | Ee-JAY MOTOR TRANSPORTS, INC | | | SCAC3 |
| 79 | EEJA | EE-JAY MOTOR TRANSPORTS INC | | | SCAC4 |
| 80 | EEJF | ESPARZA ESCARENO, JOSE FERNANDO | | | SCAC4 |
| 81 | EEL | Eagle European Ltd. | Callsign: Solace, | GB | AVCODES |
| 82 | EELA | ECONOMY ENERGY LLC | | | SCAC4 |
| 83 | EELB | ECO EXPRESS LLC | | | SCAC4 |
| 84 | EELD | ENVISION EXPRESS LTD | | | SCAC4 |
| 85 | EELE | ELITE EXPRESS LLC | | | SCAC4 |
| 86 | EELF | EURO EXPRESS LLC | | | SCAC4 |
| 87 | EELG | EBONY EXPO LOGISTICS | | | SCAC4 |
| 88 | EELI | EXTREME EXPRESS LOGISTICS | | | SCAC4 |
| 89 | EELK | ES EXPRESS LINES INC | | | SCAC4 |
| 90 | EELL | EDWARDS EXPRESS LLC | | | SCAC4 |
| 91 | EELM | ECLIPSE EXPEDITING LLC | | | SCAC4 |
| 92 | EELQ | ELITE EXPRESS LLC | | | SCAC4 |
| 93 | EELR | EEL RIVER FUELS INC | | | SCAC4 |
| 94 | EELS | ELITE EXPRESS | | | SCAC4 |
| 95 | EELU | ECO ENERHIYA LIMITED | | | SCAC4 |
| 96 | EELX | General Electric Rail Services Corp. | added 1/2000; 7/2000-7/2005 | | NAKINA |
| 97 | EELX | General Electric Railcar Services Corp. | added 10/1992; 1/1994; eliminated 1/2000 | | NAKINA |
| 98 | EELX | Itel Rail Corp. | added 4/1988; eliminated 10/1992 | | NAKINA |
| 99 | EELX | Evans Railcar Leasing Co. | added 10/1980; eliminated 4/1988 | | NAKINA |
| 100 | EELX | United States Railway Leasing Co. | 1/1980; eliminated 10/1980 | | NAKINA |
