[5] After South East Melbourne folded, Mackinnon joined the Townsville Crocodiles for the 1998–99 NBL season.

[1] In the 2000–01 NBL season, the Crocodiles made the grand final, however Mackinnon missed the series due to injury.

In the 2003–04 NBL season, he helped the Razorbacks return to the grand final,[5] where they lost 3–2 to the Sydney Kings.

[9] During the 2007 NBL off-season, Mackinnon attempted to enter the NBA after securing workouts with the San Antonio Spurs, Cleveland Cavaliers, Toronto Raptors and Miami Heat.

[citation needed] He was named Boomers captain in 2007[16] but missed the 2008 Olympic Games because of a knee injury suffered during the 2007–08 NBL season.

[18] In November 2022, he took on the role of the Bullets' interim head coach after the team parted ways with James Duncan.

[22] In September 2023, Mackinnon was appointed head coach of the Taranaki Airs in the New Zealand NBL ahead of the 2024 season.

[23][24] On 13 October 2024, Mackinnon was elevated to the Phoenix's interim head coach after the club fired Mike Kelly following a 0–5 start to the 2024–25 NBL season.