Born in Sheffield, South Yorkshire, Wilkinson is the son of former player and manager Howard Wilkinson. He played with the youth teams of Sheffield Wednesday, Sheffield United and Derby County, becoming a scholar with the latter in May 2003. He joined Hull City in January 2005, where he completed his scholarship. He signed a two-year professional contract with Hull in the summer of 2006. He joined Conference North club Harrogate Town on 9 December 2006 on a one-month loan, where he made five appearances before returning to Hull in January 2007.