It is operated by the Roman Catholic Archdiocese of San Antonio.

St. John Paul II was established in 2009, to serve the families in the New Braunfels, Schertz, and the Comal County area.

In August 2008, the Archdiocese bought 53 acres located on the corner of Friesenhahn Road and FM 482.

The school officially opened August 17, 2009 with 34 students and 10 part-time and full-time teachers under the name John Paul II Catholic High School after late Pope St. John Paul II.

John Paul II offers 11-man football, volleyball, cross country, men's and women's basketball, men's and women's soccer, swimming, track, golf, tennis, baseball, softball, and skeet shooting.