The 46th was assigned to the 13th Ferrying Group which was responsible for a region spanning El Geneine, Anglo-Egyptian Sudan, to Karachi, India (now Pakistan), and from Cairo, Egypt, to Tehran, Iran.

The secondary mission was to train new Military Air Transport Service (MATS) personnel and to make them an integral part of the squadron.

Aircrews of the 46th were deployed to assist in refueling operations during the Cuban Missile Crisis; it also sent aircraft and crews to Southeast Asia to support combat missions of SAC bombers and TAC fighters.

The 46th deployed aircraft and crews for tanker task forces operating out of Alaska, Spain, Labrador, and in the Great Lakes region.

The squadron commanders of the 46th Air Refueling Squadron from activation to inactivation were: Winfred H. Meibohm, C. Hunter Smith **, Laurence Maher, Jr **, Ronald L. Brumbaugh **, Wilson W. Howard **, Samuel E. Dyke **, Bertram G. Brunner **, Edward G. Palm **, Martin D. Klena, Frank Elliott **, Alvin W. Langford, Donald D. Luenenberg **, Richard E. Ring, Donald S. Croston, Richard L. Trail, Robert L. Hohman, Ronald B. Childers, Dale R. Liesch, William G. Manire, Richard W. Salsbury, William E. Rutter, Brian W. Horst, Russell Deming, James Nakauchi (** indicates this individual was Deceased as of Sep 2013).