He started his managerial career as player-manager with Grantham Town in 1996. He left the club after leading them to the Southern League Midland Division title in his second season. He then served as player-manager at Southern League Premier Division club King's Lynn from 1998 to 2000, which was brought to an end after he resigned. He was appointed player-manager of Southern League Premier Division club Tamworth in 2001, before leaving to join the coaching staff at Coventry City in 2002. Mills was handed his first managerial role in the Football League with Notts County in 2004, but was dismissed several months after the club was relegated to League Two. He managed Alfreton Town of the Conference North from 2005 to 2007 when he returned to Tamworth. The club was relegated from the Conference National before Mills led them to the Conference North title in 2009. He left Tamworth in 2010 to become manager of their Conference Premier rivals York City. Mills oversaw York's victories in the FA Trophy and Conference Premier play-offs in 2012, the latter resulting in promotion to League Two. He was dismissed by York in 2013 before taking over at Gateshead, and after leading them to the Conference Premier play-offs in 2014 he was named the Non-League Manager of the Year. Mills took over as manager of their National League rivals Wrexham in 2015, but was dismissed the following year.