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

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.

In fall 2009, the women's cross country team won their first NAIA National Championship.

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.