 In 2002, Wharton was promoted from assistant academy director to academy director, taking over from Alan Irvine who left to join Everton as assistant manager to David Moyes.In October 2004, following restructuring of the academy personnel, John Carver took over as academy director and Wharton assumed the role of academy coach.During the 2003–04 season, Wharton also joined the reserve team coaching staff.