1998 Wilkie came from the U-19 division of the FC Dundee, a club from his hometown to the professionals. During his time at FC Dundee he was twice briefly presented to the English clubs Plymouth Argyle and Notts County in 2001. Also at FC Falkirk Wilkie stood a short time under contract. In January 2004, he tore himself in the game against Dundee United cruciate ligament, but could not undergo surgery and so had to perform a muscle training to strengthen the cruciate ligament.
In 2006 he moved to Dundee United. Dundee coach Craig Levein held Wilkie time being not fit for the premier league and first gave it to Ross County. After Barry Robson had left in the direction of Glasgow Celtic Dundee United in February 2008, Wilkie was appointed as the new captain.
However, it was announced on April 3, 2010, that Wilkie must end his career early at the age of 29 years due to persistent knee problems.
Wilkie was under coach Berti Vogts his debut for the Scottish national team. When Reunification Cup in Hong Kong in May of 2002 Wilkie played against South Africa for the first time for Scotland. In March 2003, Wilkie scored his only international goal in the match against Iceland.
- Scottish FA Cup: Second 2002/ 03 ( with FC Dundee)
- Scottish League Cup: Second 2007/ 08 ( with Dundee United)
- Scottish Premier League: Player of the Month October 2007