In October 1945, MacFadyen was appointed as secretary-manager of
Dundee United, a position he would hold for nine years. While he led the club to a memorable Scottish Cup giant killing against
Celtic in
1949, he also oversaw United's record defeat when they lost 12–1 against the team where MacFadyen had been idolised as a player, Motherwell. He resigned from his post not long afterwards, in August 1954. The Dundee United job was to be his last in football. After leaving the game, he worked as a physiotherapist and chiropodist. MacFadyen died in 1971. His son
Ian was also a footballer who played for Dundee United's reserve side while his father was manager, then moved to Motherwell around the time Willie also left the club, returning to
Tannadice for one season in 1959. On 27 September 2022, it was announced that MacFadyen was to be inducted into the Motherwell F.C. Hall of Fame. ==Honours==