Wilkie joined the club in October on a short-term deal after leaving neighbours Dundee in the summer as he struggled to fully recover from a cruciate ligament injury he first suffered in January 2004. There were considerable fears for the 26-year-old's long-term future when he revealed that he would play on without a cruciate ligament.
After making his United debut in Craig Brewster's last game in charge - a 5-1 defeat by Falkirk - Wilkie was loaned to Ross County by Craig Levein. But the giant defender, who has 11 caps for Scotland, has been impressive at the heart of the United defence since January.
United manager Levein said: "I am delighted Lee has agreed to remain with the club for a further two years as I am positive he will make a huge contribution to United in the years ahead. Since returning to a regular first-team role, his performances have been outstanding."
Wilkie said: "I have worked hard to take advantage of the opportunity given to me by Dundee United and would like to thank everyone at the club for helping me resume my career. The manager has been excellent with me, on and off the park."