St. Francis Xavier’s College was founded in 1842 by the Society of Jesus. It was opened by Fr.Francis Lythgoe and was to be conducted by masters from and in connection with the Jesuit College at Stonyhurst, near Blackburn. 

The school at first occupied a house at 36 Soho Street, but in 1843 it moved to 43 St. Anne Street. Three years later it was established at Salisbury Street, where it was to remain until 1961. The imposing college building, which can still be seen on Salisbury Street, was erected in 1877. 

In the years immediately before the Second World War, the decision was taken to move the College from the inner city to a site in the suburbs which could accommodate both the school and playing fields. This led to the purchase of the High Lee Estate at Woolton in 1941.

 The playing fields at Woolton were brought into use in 1950 when those at Melwood, West Derby, which had been acquired in 1920, were sold to Liverpool Football Club. Eleven years later, the College moved into its new accommodation at High Lee and the buildings at Salisbury Street were sold to Liverpool City Council. 

In 1974 the trusteeship of the College was transferred from the Jesuits to the Brothers of Christian Instruction, who had come to Liverpool in 1961. They are the present trustees and continue to undertake the direction of the school. 

In 1983 the College participated in the scheme of re-organisation of Catholic secondary schools in Liverpool. The buildings of the former Cardinal Newman Secondary Modern School on Queens Drive, Childwall, became the lower school of S.F.X., while the buildings at High Lee accommodated the upper school. Since 1983 the school has had a comprehensive intake of pupils from its neighbouring Catholic primary schools. 

The opportunity for schools to opt out of local authority control was given by the Education Reform Act of 1988. In February 1989, the parents of boys at the school voted in favour of applying for grant-maintained status. The application was subsequently approved by the Secretary of State, and, in consequence, St. Francis Xavier’s College opened a new chapter in its history in January 1990, when it assumed complete control of its own management with direct funding from the Department for Education. 

The College celebrated its one hundred and fiftieth anniversary in 1992 and became a Foundation School in September 1999. From September 2002 the whole school became situated on a single site at High Lee, Beaconsfield Road.

The College acquired Specialist Status as the first Mathematics and Computing College in the City in September 2005. In 2012 the College sucesfully applied to the Department for Education to become and academy and on the 1st August 2012 the College converted into an Academy.