Duncan's first managerial job was at Scunthorpe United. His first season in charge proved to be one to forget, as they finished second-bottom of the Fourth Division and were forced to apply for re-election to the Football League. The following season was a vast improvement however, and Scunthorpe spent much of the season challenging for the Fourth Division title. However, Duncan was controversially sacked in February 1983 after it was alleged that he had spoken to Second Division side Grimsby Town about their manager's job. Scunthorpe eventually achieved promotion that season under succeeding manager Allan Clarke.
Six weeks after being sacked by Scunthorpe, Duncan was invited to become interim manager of Hartlepool United, who were bottom of the Fourth Division. In his two months in charge the club earned enough points to escape bottom place, but their eventual finish of 22nd place wasn't enough to prevent Duncan spending a second successive year watching his club apply for re-election. That summer, Duncan was offered the chance to become the club's permanent manager, but turned it down in favour of the manager's job at Chesterfield, who had just been relegated from the Third Division.
Duncan's first season in charge of the club resulted in only a mid-table finish, but in 1985 he steered the club to the Fourth Division title. The club managed to stay in the Third Division for the next two seasons, even looking like they might challenge for promotion to the Second Division in the early stages of the 1985–86 season. Duncan's achievements with the club were noticed by Ipswich Town, who appointed him as manager in the summer of 1987 following the departure of Bobby Ferguson.
In his first season in charge, Ipswich managed a decent finish but never seriously challenged for promotion. The following season saw an improvement, and they missed out on the play-offs by just three points. Duncan's third season in charge of Ipswich started badly however, and even some good results near the end of the season weren't enough to make any sort of promotion push, leading to Duncan being sacked after the season ended.
After leaving Ipswich Town, Duncan took up a career in schoolteaching in Suffolk before returning to Chesterfield, where he achieved Division Three playoff glory in 1995 and reached the F.A Cup semi finals in 1997 losing to Middlesbrough in the replay. This was achieved with impressive victories away to Bolton, and victories at home to Wrexham and (then) Premier LeagueNottingham Forest before the infamous semi-final tie with Middlesbrough at Old Trafford which ended in a 3–3 draw. Chesterfield even had a contentious goal that appeared to cross the line which was not given by Referee David Elleray. Chesterfield's last minute equaliser resulted in Duncan celebrating so wildly he lost his glasses. Chesterfield were defeated in the replay 3–0 at Hillsborough. He was to be sacked three years later upon their relegation back to Division Three. In 2002 he was given a testimonial against Manchester United in his honour.