Линфилд
Ferguson was appointed manager of Ballymena United on 30 December 2011. His first game in charge was against Linfield F.C. on 8 January 2012, and won his first trophy as manager when the Sky Blues defeated Ferguson's former club Linfield in the County Antrim Shield final on 27 November 2012. Ferguson led Ballymena United to the Irish Cup final for the first time since winning the cup in 1989 where they were beaten 2-1 in the final by Glenavon. Ferguson was sacked in 2016 and replaced by David Jeffrey.