[1] Between 2021 and 2023, Gleeson served as an assistant coach for the Toronto Raptors in the National Basketball Association (NBA).

[2] In 1990, Gleeson was appointed head coach of the Warrnambool Mermaids in the Country Victorian Invitational Basketball League (CVIBL).

[2] Following his stint with the Seahawks, Gleeson moved to Gold Coast, Queensland, to study and coach at Griffith University.

He connected with coach Bob Thornton and joined him on his staff at the Quad City Thunder in the Continental Basketball Association (CBA).

[9][10] For the 2004–05 season, Gleeson moved to South Korea to serve as an assistant coach with the Seoul Samsung Thunders of the Korean Basketball League.

[15] In April 2011, Gleeson was appointed head coach of the Melbourne Tigers in the NBL[16] on a reported three-year deal worth around $150,000 a season.

[20] In June 2013, Gleeson was appointed head coach of the Perth Wildcats in the NBL on a three-year deal.

[27] They went on to reach the NBL Grand Final series, where they defeated the New Zealand Breakers in three games to win the championship.

[32] With the signing of import guard Bryce Cotton in January,[33] the Wildcats won eight of their remaining twelve regular season games, including two must-win encounters in the final round to squeeze into the playoffs.

[37] They went on to win six straight games to lock up the minor premiership before losing the regular-season finale in overtime to Melbourne United, thus finishing with an 18–10 record.

Captain Damian Martin (calf), starting centre Angus Brandt (ankle) and back-up guard Mitch Norton (calf) missed large chunks of the season, while imports Bryce Cotton (thumb/hamstring) and Terrico White (hamstring/wrist) also missed games.

The Wildcats were under intense external pressure to make changes to their roster, including signing a third import, after going through a slump where they lost eight out of 10 games, but Gleeson refused to budge and the players responded.

[51][52] After losing back-to-back games to start January 2020, Gleeson and the Wildcats decided to release import Dario Hunt and replace him with seven-year NBA veteran Miles Plumlee.

[54] After defeating the Taipans 2–1 in the semi-finals, the Wildcats faced the Sydney Kings in the NBL Grand Final.

[60][61] In February, Gleeson coached the Wildcats for the 231st time, surpassing Alan Black to set a new club record.

[63][64] With his 250th career win later that month, he became just the sixth coach in NBL history to reach that milestone, and the third fastest to do it at 424 games.

[71][72] He guided the Wildcats to a sixth grand final in eight years with a 2–1 semi-final series victory over the Illawarra Hawks.

[75][76] On 12 July 2021, Gleeson requested to be released from the final year of his contract with the Wildcats after receiving an NBA coaching opportunity.

[80] His first game as an NBA assistant coach came on 20 October 2021 in the Raptors' 98–83 season-opening loss to the Washington Wizards in Toronto.

[89] In June 2014, Gleeson was called up to the Australian Boomers coaching staff for the 2014 FIBA Basketball World Cup.

[92] He continued on as Lemanis' assistant in 2015 and 2016, as he was a part of the Boomers' 2015 FIBA Oceania Championship triumph[93] as well as their Rio Olympics campaign.