Kelly started his coaching career with spells at York City and Sunderland, before being appointed manager of League One club Oldham Athletic in May 2015. He was dismissed in September 2015, and took over at National League team FC Halifax Town in October, before he left by mutual agreement a month later. Kelly took over at Northern Premier League Premier Division club Hyde United in March 2016, and led the club to promotion and first round proper of the FA Cup in his second season at the club.