Wheeler was elected to represent the First District in the U.S. House of Representatives. He served in the Fifty-fifth, Fifty-sixth, and Fifty-seventh Congresses (March 4, 1897 – March 3, 1903). Wheeler secured significant appropriations for projects in his district, including the expansion of a federal courthouse in Paducah and the protection of a local ice harbor. He used his influence as a member of the Naval Affairs Committee to secure the naming of the "USS Paducah". He was later chosen to give the presentation address when the city of Paducah presented a silver service for use on the ship. The Paducah Company of the Kentucky State Guard adopted the name "The Wheeler Guard" in his honor.