Some believe the school to have been founded prior to the 12th century by the Benedictine monks of Abingdon Abbey, with a legal document of 1100 listing Richard the Pedagogue as the first headmaster.

With John Roysse's re-endowment of 1563, the school moved to a site south of the Abbey gateway.

[7] After the dissolution of Abingdon Abbey in 1538 the school passed through a difficult phase: the sixteenth century endowments by Old Abingdonians attempted to overcome the loss of monastic support.

Despite being penalised during and after the English Civil War for its royalist and Anglican tendencies the school survived and achieved somewhat of a revival under headmaster Robert Jennings (1657–1683).

In 1671 ten boys were expelled after they refused to attend Anglican services at St Helen's church.

[7] The school experienced a successful period during the 18th century under headmaster Thomas Woods (1716–1753), known as "Flogging Tom".

[7] At the turn of the century the school entered a period of decline under the leadership of the "incompetent"[4] headmaster Dr John Lempriere.

[7] The current school site in the Victorian quarter of Abingdon, adjacent to Albert Park, was designed by Edwin Dolby and was built from 1870.

Mercers Court was opened in 1994 by the Chancellor of Oxford University and Visitor of Pembroke College, Baron Jenkins of Hillhead.

[19] In 2015 the Yang Science Centre, designed by Hopkins Architects, opened in October, housing 21 laboratories, study areas and prep rooms.

[20] The previous science building was refurbished in 2016, with new rooms for history, geography and classics and new sports facilities were installed at Tilsley Park.

[21][22] In 2018 a new development called Beech Court, housing a new library, Sixth Form Centre and art facilities was completed and opened in November.

[31] Abingdon's core sports are rowing, rugby union, football, field hockey and cricket.

[32] The school won the Princess Elizabeth Challenge Cup at Henley Royal Regatta three years running, in 2011, 2012 and 2013, and has recently reached the later stages of the Daily Mail U18 rugby cup whilst also gaining places in the last four of the HMC national 20/20 cricket competition.

[35] The School's Edmund and Roysse Societies hold talks for several times a term, inviting speakers to lecture on a variety of subjects.

[45] The Foundation Dinner, to honour the school's founders and benefactors, is held once a year towards the end of Lent term.