Cockburn and Horner recruited John Russell as a co-founder and the three of them, together with other interested parties, put a proposal to the City Council for the building of a new school.

[12] On 27 July 2022, broadcaster Nicky Campbell disclosed that he had witnessed and experienced sexual and violent physical abuse while a pupil at the Edinburgh Academy in the 1970s.

[18] When actor Iain Glen spoke out about his abuse in 2002, "the wrath of Morningside and Muirfield and Murrayfield rained down on his head with biblical fury because he'd broken the code, the Edinburgh omertà".

[19][20][21][22] Also frequently mentioned was Hamish Dawson, deceased, whose affectionate appreciation from the Rector in September 1984 was contradicted by testimony from many reporting having suffered at his hands.

[27][28] On 12 December 2023, Police Scotland announced that five former teaching staff aged between 69 and 90 had been arrested for questioning regarding alleged abuse incidents between 1968 and 1992, with one further individual to be referred to the authorities.

[29][30] On 11 March 2024 at Edinburgh Sheriff Court, an examination of facts hearing regarding John Brownlee commenced as, at 89 and demented, he was deemed unfit to stand trial.

[31] On 27 March, after over two weeks' testimony from 42 former pupils, the Sheriff ruled that Brownlee had repeatedly committed a number of violent assaults against children aged between eight and 11 years, spanning 31 charges as well as ‘cruel and unnatural acts’ at the school.

[37] Famous alumni of the school include Robert Louis Stevenson, James Clerk Maxwell, Nicky Campbell, Magnus Magnusson, Baron Falconer of Thoroton, Mike Blair, and Iain Glen.

It has also produced one Nobel Prize winner (J. Michael Kosterlitz), numerous political and legal figures, several rugby internationals and nine recipients of the Victoria Cross; the highest number of any school in Scotland.