In December 2008, Parkinson was confirmed as the new Charlton manager, and Kinsella assumed the role of first-team coach permanently. He was sacked along with Phil Parkinson on 4 January 2011. He was linked with return to his former club Colchester United as manager in August 2009, but the job went to Adrian Boothroyd. He became manager of Daventry Town in June 2011, leaving the club in July 2012. Having left Daventry, Kinsella joined former St Neots Town manager Dennis Greene's coaching staff at Conference North side Histon in August 2012. Mark was appointed Colchester United assistant manager on 27 September 2012, to work alongside fellow Irishman Joe Dunne. On 1 September 2014, Mark Kinsella was sacked as assistant manager of Colchester United. On 29 November 2014, Kinsella was announced as assistant manager of League of Ireland side Drogheda United. Kinsella replaced Johnny McDonnell as manager following McDonnell's departure from the club after a 4–1 home defeat to bottom side Limerick.