St Francis Xavier High School was founded 1976. The school began at Catholic Girls High School Braddon, now Merici College, as the Florey building wasn’t ready to be occupied. In the first year there were 74 Year 7 students who made up the two classes. The Foundation principal was Mr Jim Smythe. SFX, as it affectionately known, was the first lay-run Catholic High School in Canberra. Apparently every religious teaching order in Australia had passed up the opportunity to staff the new venture.

The school moved to its permanent site in Florey in 1977. Year 7 and Year 8 were joined by students in Years 5 & 6 from what was to become St Monica's Primary School in Evatt. St Monica’s was still under construction so SFX provided temporary accommodation for the St Monica’s students – many whom would come to SFX for High School.

Mr Peter Moore took over as Principal in 1977 (until 1984) and began the difficult task of creating a 'St Francis Xavier identity'. He commissioned the school's crest and motto. He then set about the task of supporting and encouraging his new charges in the path of 'truth and courage'. Francis Xavier was chosen as the Patron Saint with the school crest and motto incorporating both his name, his Christian commitment and the ideals of truth and courage reflected in his life. The school crest was designed by Mr C Uilricks. The logo identifies the school through the intertwined initials of its patron saint. The bar of the F forms a cross, the sign of Christ 'the author of our faith' - Hebrews 12.2.

In 1982, with Belconnen flourishing, the demand for places far exceeded capacity and enrolment guidelines were introduced. In a number of years there were in excess of 1000 students, in Years 7 to 10, at the school. Mr Jim Peoples was Principal from 1985 to 1992, followed by Acting Principal Mr Allan Cope in 1993.

The possibility of extending SFX to Years 11 and 12 was first discussed in the early 1980s. There were questions as to whether there would be enough Senior enrolments and the proposal was shelved. The issue never went away and in 1997, under Principal Mrs Moira Najdecki, a new plan was formulated and presented to the Catholic Education Office. St Francis Xavier College was born. Mrs Moira Najdecki (currently the Director of the Catholic Education Office, Canberra) was Principal from 1994 to 2002.

The imminent increase in numbers fostered a flurry of building activity. A new Maths block was built next to the oval and the old Maths staffroom was converted to a Senior Study/Vocational Education room. The Resource Centre was extended and refurbished. The Industrial Arts area was expanded. A new Senior common room was also added. The first Year 11 students started in 2001 and the first Year 12 graduation was in December 2002, the same year that SFX held its Silver Jubilee celebrations.

In 2003 Mr Angus Tulley was appointed Principal and he has endeavoured to keep the spirit of St Francis Xavier College alive. He actively encourages students to reach their full potential, and provide a learning environment where they are supported and encouraged. Mrs Sue Sturgiss was Acting Principal in 2010. Under Mr Angus Tulley’s leadership the College has added a Trade Training Centre, a purpose built Middle School Building, the refurbishment of the Religious Education corridors – incorporating breakout areas with an emphasis on IT facilities and the new Student Services Hub – linking the IT rich Resource Centre with new Canteen and Café facilities.

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