Duffy was appointed temporary manager of Clyde on 6 February 2011. Duffy appointed his former Partick Thistle teammate Chic Charnley as his assistant two day later. He succeeded in lifting Clyde off the bottom of the Third Division briefly, but finished the season last, and agreed to stay with the club for the 2011–12 season. He was appointed permanent manager on 28 April 2011. Duffy chose to stay at Clyde because of job security in a time where an average managerial reign at a club in Britain lasts approximately less than 15 months and in agreement with the Clyde board, progression on the field would take time for the club .