In 2006, he left San Antonio to become a Dallas Mavericks assistant coach, becoming a part of the staff of former Spurs player Avery Johnson.
[7] The team ended the 2006–07 season with the best record in the league, led by MVP Dirk Nowitzki, but were upset in the first round of the playoffs by Don Nelson's Golden State Warriors.
[8] Prunty left the Mavericks for the Portland Trail Blazers[9][10] in 2008 when Avery Johnson was fired[11] and replaced with Rick Carlisle.
[13] Nets' head coach Jason Kidd was suspended for the first two games of the season after pleading guilty to a misdemeanor DWI charge stemming from an incident in July 2012.
On December 23, 2015, Prunty was named the interim head coach for 17 games as Kidd underwent hip surgery.
[19] After winning that game, for the rest of the season onward, the Bucks would improve just enough to gain the 7th seed of the Eastern Conference in the 2018 NBA Playoffs, facing against the Boston Celtics in the first round.
[22] On June 23, 2021, Suns coach Monty Williams credited Prunty as being a partial inspiration for a Western Conference Finals game-winning inbounds alley-oop play set up between Jae Crowder and Deandre Ayton.
[24] With McMillan and lead assistant Chris Jent entering health and safety protocols, Prunty served as acting head coach[25] for three games of a west coast road trip in January 2022.
[27] For the Hawks' 123–122 dramatic overtime victory against the Chicago Bulls on December 11, 2022, Prunty drew up the play that led to AJ Griffin sinking a game winning layup with 0.5 seconds left on the clock.
[31] On June 28, 2023, it was revealed that Prunty would rejoin the Milwaukee Bucks as an assistant coach, joining Adrian Griffin's staff.
[34] Prunty was named the head coach of the Great Britain men's national team in June 2013 after an extensive interview process following Chris Finch's resignation.
Despite being without top players Luol Deng, Ben Gordon, Joel Freeland, and Pops Mensah-Bonsu, Prunty began his tenure with a 61–55 win over Puerto Rico in an International Test Match at The Copper Box Arena, London.
[41] Due to changes from FIBA in the qualifying process for the upcoming World Cup and Olympics that conflict with the NBA,[42] Prunty was forced to step down as head coach of the Great Britain men's national team after Eurobasket 2017.