[6] Thompson was restricted by age and injury to just eight appearances for Essendon during the 1996 AFL season, his last match was the night the lights went out at Waverley Park in round 10.

[8] In 1999, Thompson joined the North Melbourne Football Club as an assistant coach under senior coach Denis Pagan in what became a premiership year for the Kangaroos in the 1999 season, when North Melbourne defeated Carlton in the 1999 Grand Final to win the premiership.

The following year in the 2005 season, the club under Thompson finished sixth and was beaten in the Semi-Finals by 3 points against the eventual premiers Sydney Swans after leading for the majority of the match.

Thompson coached Geelong to win the AFL premiership in the 2007 AFL Grand Final by more than 100 points, which was the highest winning margin in Grand Final history, against Port Adelaide Football Club at the MCG on 29 September.

In an upset, though, Hawthorn beat Geelong under Thompson by 26 points in front of 100,012 fans in the 2008 AFL Grand Final.

[18] During an end-of-season holiday to New York that year, Thompson ran into Melbourne Storm coach Craig Bellamy whilst inside a hotel.

On 26 September 2009 in the 2009 AFL Grand Final, Geelong under Thompson faced a St Kilda side determined to break its 43-year Premiership drought.

In front of 99,251 fans on a rain-soaked MCG deck, the Cats under Thompson clawed their way back after trailing at every break to win the AFL premiership by 12 points.

This would be Geelong's second flag under Thompson in three years cementing their place as one of the great teams of the modern era.

Thompson as always was magnanimous in victory and accepted the AFL Premiership trophy alongside Geelong legend Bob Davis.

[20][21] After Geelong under Thompson were eliminated from the preliminary finals to Collingwood, at the conclusion of the 2010 season, on 4 October 2010, Thompson announced his retirement and resignation as Geelong Football Club senior coach effective immediately, his reason being that he was "tired of coaching" after a decade at the helm.