Following Megson's sacking as Stockport County boss on 25 June 1999, Andy Kilner took over as manager. Phelan moved on shortly afterwards, taking up a role at Manchester United's Centre of Excellence. With Steve McClaren's departure to Middlesbrough in the summer of 2001, Phelan was promoted to first-team coach. He was appointed assistant manager of Manchester United on 3 September 2008, replacing Carlos Queiroz who had left to manage the Portugal national football team. For many seasons, Phelan was seen conducting interviews with BBC programmes such as "Match of the Day" due to United manager Alex Ferguson refusing to speak with the BBC following corruption allegations made in 2004 by the BBC's "Panorama" programme towards one of Ferguson's sons, football agent Jason Ferguson. Ferguson finally agreed to BBC interviews once more in August 2011.