Wilkie then signed for Dundee United and he again played regularly for a while, but ongoing knee problems forced his retirement from professional football in April 2010.
Unable to receive an operation, he hoped to continue playing professional football by strengthening the knee muscles to compensate for the lack of ligament.
In early-November 2006, new manager Craig Levein stated his intention to send Wilkie out on loan for "about a month", feeling he was "not ready to play first-team matches at this [SPL] level.
[8] On 1 February 2008, following Barry Robson's move to Celtic, Wilkie was named captain; six weeks later, he led the team out at Hampden Park for the 2008 Scottish League Cup Final, where he was one of three players to miss a penalty in the defeat to Rangers.
Wilkie's last international appearance was an unhappy experience, as the Scots suffered a 6–0 defeat against the Netherlands in November 2003 that ended their hopes of reaching UEFA Euro 2004.