 McQuilken moved on to Aberdeen in June 2003 but was made available for transfer in January 2004 and within days, McQuilken moved to St Johnstone.At the start of the 2004–05 season, he moved to Gretna on a six-month loan deal which was subsequently made permanent.After suffering a heart scare in September 2006,
McQuilken moved to Dumfries club Queen of the South in January 2007.