Born in Manchester, Doherty started his professional career with Manchester United in 1952. He was part of the United squad that won the 1955–56 league title and scored seven goals in 26 appearances. In October 1957, he was transferred to Leicester City for £6,500. His exit from Old Trafford came just before eight of his United colleagues lost their lives in the Munich air disaster; he was in a Leicester hospital undergoing surgery for a knee injury when he heard the news.
He left Leicester after only one season due to his knee related problems, before moving on to Rugby Town, and then to Altrincham.
In the autumn of 1958, when Arsenal made an offer to Manchester United assistant manager Jimmy Murphy to become their new manager, Murphy offered Doherty the chance to become his assistant if he took charge at the North London club. However, Murphy then decided against moving to Arsenal and the partnership never happened