From 2012 to 2020, the team was a member of the Great Northwest Athletic Conference of NCAA Division II.

Prior to the 2012 season, the Cougars had been an independent program in the NAIA.

[3] Azusa Pacific University decided to end its football program in December 2020 due to financial restructuring.

The Cougars appeared in the Division II playoffs two times with an overall record of 0–2.

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