In 1995, he was posted to the 2nd Battalion, The Royal Canadian Regiment as Officer Commanding G Company, leading them as part of the Queen's Royal Hussars Battle Group on the initial NATO mission in Bosnia. In 2000, Major-General Thompson assumed command of the 3rd Battalion, The Royal Canadian Regiment returning to Bosnia in 2001 as the Battle Group Commander.
On leaving Regimental duty in 2002, he took up a post as a policy officer including a secondment to Foreign Affairs Canada. In 2006, Major-General Thompson was appointed Brigade Commander of 2 Canadian Mechanized Brigade Group in Petawawa until assuming command of Task Force Kandahar from May 2008 to February 2009. Afterwards, he served in a number of staff positions at National Defence Headquarters before being appointed Commander of Canadian Special Operations Forces Command in 2011.
On 3 March 2014, Major-General Thompson assumed command of the Multinational Force and Observers in the Sinai Desert of the Arab Republic of Egypt.
He is married to her Excellency Mme Isabelle Roy, Canada’s Ambassador to Algeria, and has two adult sons, Philip and Christopher.