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The University established the Tuks Football Academy in 2002, originally playing in the SAFA Gauteng South Division. In the 2003–04 season the University acquired Pretoria City FC's second division status, subsequently winning the Vodacom League play-offs and being promoted to the NFD in 2004–05. In the 2006–07 season the club qualified for the Mvela Golden League play-offs. In the 2008–09 season the club was a Nedbank Cup finalist losing to Premiership team Moroka Swallows 0–1.
Following the 2011–12 season University of Pretoria gained promotion to the Premiership with Stephen Haupt as the head coach.
In the 2014–15 season they finished 13th in the Premiership, and the following 2015–16 season they finished 15th. They finished at the bottom of the Promotional Playoff log without a win and were relegated to the NFD. In the 2016–17 season they finished 12th in the NFD. The following 2017–18 season saw a slight improvement, finishing 10th, and the 2018–19 season saw the club finish 14th in the NFD.
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