After his retirement as a player, Wilhelm managed two minor league teams in the Atlanta Braves system for single seasons. He led the 1973 Greenwood Braves of the Western Carolinas League to a 61–66 record, then had a 33–33 record with the 1975 Kingsport Braves of the Appalachian League. He also worked as a minor league pitching coach for the New York Yankees for 22 years. As a coach, Wilhelm said that he did not teach pitchers the knuckleball, believing that people had to be born with a knack for throwing it. He sometimes worked individually with major league players who wanted to improve their knuckleballs, including Joe Niekro. The Yankees gave Wilhelm permission to work with Mickey Lolich in 1979 even though Lolich pitched for the San Diego Padres.