The school was originally the Hospital of St. James and St. John, founded around 1150 by Robert le Bossu, Earl of Leicester. In 1484 it was given to Magdalen College, Oxford, by 1548 there was a school at the site. The school's initial purpose was to allow pupils of the college in Oxford to escape the plague affecting Oxford at the time. In September 1973 Magdalen College School merged with the Girls Grammar School (Brackley High) and Brackley Secondary Modern School to form a new comprehensive school on two sites, while the girls' school was converted into the new Southfield Primary school.

Many of the school buildings are listed, including the school chapel the earliest datable parts of which are late12th century. The chapel underwent a major restoration 1869–1870 by Buckeridge. It is constructed of stone rubble and is the oldest school chapel still in use in England. It remains in regular use by the school, Church of England and local community.

In January 2013 we became an Academy and look forward to building on our successes and developing the opportunities further for our students. Our link with Magdalen College Oxford continues today with 4 foundation governors from The College supporting our work alongside parent, staff and community governors to provide us with a broad governing body committed to supporting our work to provide an excellent education for our students now and into the future.