McCall was part of the coaching staff during his second spell at Bradford City, briefly serving as caretaker-player manager in 2000. He continued his coaching at Sheffield United and was assistant manager to Neil Warnock until May 2007, when he returned to Bradford City for a third time, this time as manager. He spent two-and-a-half seasons in charge of Bradford City, leaving in February 2010. Just before the end of the year, he took over as Motherwell manager.