Over its history, the school occupied various parts of the present-day Magdalen College, firstly the low hall south of the Chapel of the Hospital of St. John the Baptist, which before the establishment of Magdalen College by William Waynflete had occupied the present site.

It was slowly relocated by a few hundred feet, over Magdalen Bridge, onto the present site on Cowley Place began under the tenure of W. E. Sherwood in 1891 when, after an outbreak of scarlet fever in the old boarding house on the corner of Longwall Street and the High Street (ascribed partly to the dilapidated state of the building and in particular to the drainage) plans for a new school house were laid out.

The choristers still today make this short daily journey, but using a tunnel under Magdalen Bridge to avoid crossing the busy road.

A new school chapel was added to the 1928 buildings at the Milham Ford end, paid for by Old Boys, and was furnished with stained glass from the original chapel on Longwall Street, portraits of former Masters, Ushers, and Old Waynfletes (men educated at the school), and with an old organ built by Binns of Bramley, near Leeds.

Whilst £8,000 was promised by the end of the year, the outbreak of the Second World War curtailed any further fundraising or large-scale building for its duration.

Under the mastership of Kennard Davis, the period of the war was marked by an increase in the school's numbers, caused in part by the relative safety of the city of Oxford, while the Officers' Training Corps, precursor to the present-day Combined Cadet Force, "played its part in the defence of Oxford against possible enemy parachutists and fifth-columnists, guarding the river banks at night with fixed bayonets!".

This plan was never set into motion, and in 1957 the school built new laboratories, on the Plain roundabout end of the site, now housing both science and Design & Technology facilities.

In 1959, a movement began towards constructing the present-day Big School building, which was designed by Booth, Ledeboer, and Pinckheard and eventually opened in 1966.

[11] The new building was hexagonal, with a stage and orchestra pit at one end and an altar (given by Magdalen College) in a chapel area at the other, as well as an acoustic-panelled ceiling and a cluster of lighting.

By the late 1960s, the school's status as a direct grant scheme member came under threat as sweeping changes were made to the then Tripartite System.

On 20 March 2007, David Brunton, head of media studies and English teacher at the school, was found dead at the base of St Mary the Virgin Church tower in Radcliffe Square,[12] Oxford.

They are: School Field, an island in the River Cherwell originally leased from Christ Church in 1893,[14] and connected by 'willow-pattern' bridges to the School House rose gardens, provides space for field sports such as cricket, rugby and football, as well as lawn tennis.

Many instruments are taught, and ensembles catering to a wide variety of tastes and styles operate on a weekly basis, performing regularly.