Burke made the move to the CFL as the defensive backs coach with Calgary Stampeders from 2005 to 2007. He later joined the Montreal Alouettes as defensive coordinator under head coach Marc Trestman from 2008 to 2010, where he won two Grey Cups. In 2011, he took over as defensive coordinator for the Blue Bombers. The next year, Burke interviewed for the vacant Hamilton Tiger-Cats head coaching position, but did not get the job. He returned to the Blue Bombers for the 2012 season and was promoted to interim head coach on August 25 following the dismissal of Paul LaPolice.[2] At the end of the season, the interim tag was removed and the Blue Bombers officially named Burke the 29th head coach in team history.[3]
Burke was fired by the Blue Bombers only a year later, after the team finished last in the league with only three wins.[4] Shortly after, the Toronto Argonauts hired Burke as their new defensive coordinator.[5] Burke left the Argonauts after one year for personal reasons.[6]