Upon his return back to the United States and graduation, Whelchel was assigned to the football coaching staff. He served there until 1927, when he was transferred to the battleship USS Florida. He also coached their football squad. In 1930, his next service assignment was Norfolk Naval Shipyard, where he became coach of the local Navy football team. Subsequently coached football team on the board of USS Idaho.
Whelchel returned to the Naval Academy in 1941, where he became backfield coach of local football team. Next year he succeeded main coach Swede Larson. Whelchel led the Navy team to a 5-4 record in season 1942 and an 8-1 record. He also won the Lambert Trophy in season 1943.