The Seton Hall Prep Pirates compete in the Super Essex Conference, which is comprised of public and private high schools in the county and was established following a reorganization of sports leagues in Northern New Jersey by the New Jersey State Interscholastic Athletic Association (NJSIAA). Prior to the NJSIAA's 2010 realignment, the school had competed as part of the Iron Hills Conference, which included public and private high schools in Essex County, Morris County and Union County. With 1,454 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 IV for football for 2018–2020.