Rae started his playing career with Dundee, making over 200 league appearances for the club. He moved to Rangers in January 2004, but struggled to hold down a regular place in their team due to injury. He moved to Cardiff City in 2007 and featured regularly in the team that reached the 2008 FA Cup Final. Rae left Cardiff in 2011 and had spells later in his career with Dundee and Aberdeen. He also won 14 caps for Scotland between 2001 and 2009.