After the conclusion of the war, he transferred to Derby County, with whom he won the FA Cup, scoring a goal in the final itself as Derby beat Charlton Athletic 4–1 at Wembley Stadium. In December 1946, Doherty moved to David Steele's Huddersfield Town for a fee of over £9,000 after requesting a transfer. Doherty was unhappy with the directors who opposed his plan to secure his future by taking over the Arboretum Hotel and an earlier dispute over FA Cup Final tickets. The "Terriers" boasted a powerful front five of Albert Bateman, Jimmy Glazzard, Alf Whittingham, Doherty and Vic Metcalfe. However a weak defence saw them struggle in the lower reaches of the First Division throughout the 1946–47 season, 1947–48 and 1948–49 seasons. At Leeds Road he scored 33 goals in 83 league appearances, finishing as the "Terriers" top-scorer in his final two seasons under George Stephenson.