The St. Thomas Aquinas High School Trojans compete in the Greater Middlesex Conference, which is comprised of public and private high schools in the greater Middlesex County area and operates under the supervision of the New Jersey State Interscholastic Athletic Association. Sports offered for men include: baseball, basketball, bowling, cross country, football, golf, lacrosse, soccer, swimming, tennis, wrestling, and winter and spring track. Women's sports include: basketball, bowling, cheerleading, cross country, golf, gymnastics, lacrosse, soccer, softball, swimming, tennis, volleyball, and winter and spring track. With 510 students in grades 10-12, the school was classified by the NJSIAA for the 2019–20 school year as Non-Public A for most athletic competition purposes, which included schools with an enrollment of 381 to 1,454 students in that grade range (equivalent to Group II for public schools). The school was classified by the NJSIAA as Non-Public Group III for football for 2018–2020.