After a successful spell as Hull Kingston Rovers's Academy boss he took over the first team in 2002, winning the Northern Rail Cup and reaching the quarter-finals of the promotion play-offs.
When he was appointed at the start of the 2006 season he immediately helped the Eagles by bringing in players from the Hull area and from the student game.
The team took time to gel but eventually finished second in National League Two after an eleven-game unbeaten run, qualifying for the play-offs.
His first game in charge was against the Sheffield Eagles at the Don Valley Stadium and Wilkinson's team recorded a victory by 24 points to 20.
In May 2007 Doncaster entered into a CVA to avoid potential liquidation and Wilkinson was told not to continue as coach.