The Franciscan School of Theology (FST), is the only freestanding Franciscan graduate theological school in North America dedicated to the Franciscan intellectual tradition. An independent, accredited institution, it enjoys a service and curricular affiliation with the University of San Diego. FST is located on the campus of University of San Diego.

Rooted in the Franciscan tradition, FST is a place where the issues and concerns of society intersect with theological education. Academic development, community life, prayer and worship, and social justice are integral parts of FST. In addition to preparing Franciscan friars and other seminarians for ordained priesthood, FST is committed to the academic and professional preparation of lay ministers for leadership in today's Church. FST educates both the head and heart in the spirit of St. Francis and St. Clare of Assisi.

The Franciscan School of Theology recently announced a new online Master of Theological Studies – Franciscan Theology (MTS). It is a two-year academic program offered by the Franciscan School of Theology in partnership with the University of San Diego. Designed for working professionals and recent undergraduates alike, this unique online program is ideal for those pursuing careers in religious education, parish support, or ministry, or as preparation for further academic work. The MTS degree program also welcomes those seeking a deeper understanding of faith-based service.