On 5 July 2012, Allen was appointed manager of Gillingham signing a two-year contract. Often referred to by his nickname of "Mad Dog", Allen oversaw the Kent side's best ever start to a league season. He also broke the club record for most away wins in a football league season with a 1-0 win over Chesterfield, the eleventh of the season on 23 February 2013.On the 6th April 2013 Gillingham secured promotion to League One.