St. Francis Xavier Seminary was founded with the intention of providing a space for the Xaverian International Theologate. It was the Xaverian community for theological formation until the year 2011 when the theologians moved to Novaliches. Since then, this seminary has become the formation community for Filipino seminarians who are at the beginning of their formation process.

The community is constituted by Fr. Francisco Javier, SX, Fr. Handrianus Masri, SX, Bro. Michael Thimoty, SX, nine seminarians who are currently studying Bachelor of Arts Major in Philosophy at St. Anthony Mary Claret College (SAMCC) in Culiat, Quezon City, and one student in propaedeutic. 

The St. Francis Xavier Seminary Community is currently having an apostolate in two chapels: Ina ng Laging Saklolo (Our Lady of Perpetual Help) of Sitio Militar, and San Jose chapel.