The Cougars compete in NCAA Division II as a member of the California Collegiate Athletic Association (CCAA).

However, the mascot was "dropped for something with more ring," and in a referendum students selected "cougar" over "mountain lion."

The dropping of the indigenous word was criticized by a faculty member at CSU San Marcos.

Jim Saia was the first men's basketball head coach, who led the team to the NAIA Division I National Championship Tournament in 2012–2013.

The Cal State San Marcos Cougars competed in the NCAA Tournament across 2 active sports (2 women's) 2 times at the Division II level.