The first group of Catholic students to become a chartered organization was the Newman Club in the early 1950s. From then and until about 1992, the group met in an old house on 7th Street that the Diocese of Austin had purchased for the group.

During the 1980s the Diocese decided that the needs of the Baylor Catholic population would best be met by making the Newman Club into a ministry of St. Mary's of the Assumption Church in Waco. Thus, the Catholic Student Association was officially born. Fr. Jim Chamberlain, Associate Pastor of St. Mary's, became the group's first director and celebrated their first Mass with them.

Later, Fr. Bob Scott and Dcn. Joe Weynand served the student group alongside each other, followed by Fr.Jim Deaconson as chaplain and director.

In 1992, the Catholic Student Association moved into the Methodist Student Center on Speight Avenue, with Fr. Frank Miller as the regular celebrant of the Mass. With the establishment of the Marist Fathers community in Waco in 1998, Fr. Kevin Duggan and Fr. John Ulrich became regular celebrants for the group.

In 1999, the Diocese of Austin built the students a new facility. The Catholic Student Center (located on 9th Street) was dedicated by Bishop John McCarthy on October 10, 1999, and is currently the home of the now Baylor University-recognized Catholic Student Association.

In 2001, Fr. Jim Deaconson returned to the Catholic students at Baylor as the full time chaplain of the center. He served in this capacity until 2007 when he was reassigned to other pastoral duties.

Thereafter, the newly named St. Peter Catholic Student Center was assigned two priests by Bishop Gregory Aymond - Fr. Karel Fink and Fr. Anthony Odiong. This team ran the center for the year 2007. In 2008, Father Anthony was appointed full time chaplain and served until 2012.

In July of 2012, Fr. Daniel Liu was appointed by Bishop Joe Vásquez as the new director. Father Daniel served until July 2019.

In 2019, Fr. Augustine Ariwaodo was appointed by Bishop Joe Vásquez to serve as the director of the Student Center, and a year later on July 6, 2020, had the title of Rector and Chaplain of the Center conferred by Bishop Joe Vásquez.

In 2021, effective July 5, Fr. Henry Finch appointed as rector of St. Peter Catholic Student Center by Bishop Joe Vásquez.