The school began in September 1990 in a temporary site. After two years, the staff and students moved into the permanent building. As part of the Dufferin-Peel portable replacement plan, the school received a three-floor, twenty-two room addition. The project was completed in June of 2001. Currently, the school is home to almost 2000 students with more than 100 instructional staff, support staff and a childcare centre. ​

The school was named after the greatest Catholic missionary of modern times:

St. Francis Xavier, Spanish San Francisco Javier or Xavier, (born April 7, 1506[;] died December 3, 1552[;] canonized March 12, 1622; feast day December 3) [...] was instrumental in the establishment of Christianity in India, the Malay Archipelago, and Japan. In Paris in 1534 he pronounced vows as one of the first seven members of the Society of Jesus, or Jesuits, under the leadership of St. Ignatius of Loyola.

Britannica