His first job as a manager was at Shelbourne where he won the league in 2003, 2004 and 2006. In that time they also made history by managing the first Irish club to reach the third qualifying round of the Champions League, where they were knocked out by Deportivo de La Coruña from Spain. He left Shelbourne at the end of 2006.
He was made the Derry City manager at the end of 2006 but left halfway through the 2007 season after making a poor start with his new club.
He was made manager of Bohemians in early 2008 and so far has won back-to-back titles, an FAI Cup and a League Cup. He has stated that his desire is to get Bohemians into the Champions League group stages in 2010.