Deehan's absence from football did not last long. He began the 1995–96 season as manager of Wigan Athletic in the Football League Third Division, and after two seasons at the helm he guided them to the Division Three title and promotion to Division Two. After safeguarding Wigan's survival in 1997–98, he accepted the assistant manager's job at Sheffield United and for one season worked under Steve Bruce. Deehan's time at Bramall Lane was unsuccessful and he resigned after the club failed to get near the Division One playoff places.