Founded by royal charter in 1571, the school occupied several sites in Southwark, before establishing a location on Tooley Street in 1893.

In 2017, parents threatened legal action against the policies applied by headteacher Aydin Önaç (who subsequently resigned), and the London Borough of Bromley instituted an inquiry whose critical report was published in July 2018.

[citation needed] Until the school relocated to Orpington, it used to provide the choir for Southwark Cathedral through its connection to the St Saviour's foundation.

However, the Charity Commissioners required that activities and intended beneficiaries related to Southwark had to be continued to be provided for by [clarification needed] the Foundation, which supports the Cathedral choir today.

[citation needed] A new lease for the parish church of St Saviour’s dated 16 June 1559 included a pledge to start a school within two years.

[10] Henry Leeke, a Southwark brewer, left a will (13 April 1560) which gave £8 a year towards the founding and maintenance of a new free school.

In November 1560, notice to quit was given to tenants of the rooms which were to be used for the school, and in July 1561 the church wardens of St Olave’s were ordered to receive Leeke’s legacy, and "prepare" a schoolmaster by Michaelmas Day.

This new building was soon deemed to be unsuitable due to the fact that it was designed for a system of teaching which fell out of favour, and had almost no provision for classrooms.

[6][12] On 11 May 2016 a petition was set up by students objecting to new, harder sixth form entry requirements; it gained over 1,000 signatures in two days.

[18] It emerged that headteacher Aydin Önaç and bursar Alan Wooley had set up a business earlier in 2016, with the knowledge of the governors, where they were registered as the sole shareholders.

[19] On 19 October 2017 the new chair of governors, Paul Wright, announced that the headteacher had been suspended "without prejudice" while an inquiry ("in respect of concerns that have been raised over recent weeks") by the Bromley London Borough Council took place.

[23][24] Freedom of Information requests revealed that 72 students had been forced out of the school during their A-level studies since Önaç became head in the 2010-2011 academic year.

[22] The report of Bromley council's independent inquiry, led by educationalist Christine Whatford, was published in July 2018, and accused St Olave's of illegally treating its students as "collateral damage" in the pursuit of its own interests.

It called for a root and branch makeover at the school after exposing multiple cases of maladministration, said Bromley council and the Diocese of Rochester should apologise to affected parents, and urged the school to scrap its policy of restricting access to the upper sixth form, it questioned Önaç’s claims that he did not know the exclusions were potentially illegal.