[4] After his retirement from playing, Thomas coached Old Xaverians in the VAFA in 1992 and was the chairman of selectors at the North Melbourne Football Club in 1993 under Denis Pagan.
[7][8] Thomas had a focus on 'man-management' in his coaching style, as well as conducting practices on the running of the club that are common in the business world.
In early 2002, with the team having come off a 122-point loss to Geelong and with players such as Aaron Hamill, Fraser Gehrig, Heath Black, Robert Harvey, Peter Everitt, Stewart Loewe, Nathan Burke and Justin Koschitzke sidelined through injury or suspension, Thomas decided to implement an extraordinary game plan in a match against Sydney which involved flooding the Swans' forward line and continually denying them the ball by kicking towards the boundary line when there were few options forward.
The result was an 8.8 (56)–all draw, with Nick Riewoldt winning an AFL Rising Star nomination for his breakout performance.
[10] While he initially came under fire for refusing to use the 'flood', Thomas slowly started to integrate the defensive style into his match-day approach with improved results.
Despite the criticism, Thomas maintained an impressive win–loss record against some of league's most highly rated coaches, including Malthouse, Pagan, Eade, Matthews, Wallace and Craig.
[2] The decision was a shock to the football world considering that Thomas was only the second senior coach to lead the Saints to three consecutive finals series.
[12][13][14] It is not known why he was sacked, but many factors include the controversial match against Fremantle in Round 5, 2006 in which the Saints were stripped of two points following a hearing the following Wednesday, which ultimately cost them a top-four spot and the double chance, the long-term injuries to Justin Koschitzke, Aaron Hamill, Lenny Hayes and Fergus Watts and starting the season with two interstate trips in four weeks.
Together with media personality Sam Newman and decorated media journalist and TV personality Mike Sheehan, Thomas releases a weekly podcast on a wide range of global and domestic topics and current events, with a sprinkling of AFL sport comments and opinions.