 In 1989, a knee injury cut short his playing career and Wharton worked for a short period in the Probation Service before getting the opportunity to get back into football with St Johnstone, working under John McClelland.Middlesbrough then offered Wharton a part-time job as coach to their first team, this later became full-time and he graduated to their under 19s, working very successfully with a number of players who later were to progress to the first team.Wharton returned to Newcastle in 1999 and worked in tandem with former academy director Alan Irvine.