As speculation of a move to Hibernian came to nothing (despite his being installed as the bookmaker's favourite), Gannon instead was confirmed as manager of Scottish Premier League side Motherwell at the end of June 2009, two days before the club's Europa League first round qualifying tie against Llanelli of Wales. To do this he fended off competition from Aidy Boothroyd, Lawrie Sanchez, and Steve Staunton. At the start of his reign he had a limited squad, and had to draft in youth players for the Llanelli game. The club had sold off some of their best players, whilst loan deals had ended for others. He also brought in Peter Ward as assistant manager.