It was conducted in great secrecy, and was for boys of preparatory-school age who intended to proceed to the English College to complete more advanced studies.

Twyford was closed in 1745 on account of anti-Catholic feeling caused by the Jacobite rising, but Bishop Richard Challoner re-established the school in Hertfordshire at Standon Lordship in 1753, in a property owned by the Aston family.

Professors and students came back to England, where Relief Acts had considerably relaxed the penal laws against Catholics.

John Douglass, Vicar Apostolic of the London District, realised that the time had come to replace the English College, and the earliest refugees joined the students at Old Hall Green Academy.

A gift of £10,000 from John Sone, a Hampshire Catholic, enabled St Edmund's to be established in new buildings, designed by James Taylor of Islington, who had himself been a student at the Old Hall Green Academy.

Strachey, in his Eminent Victorians, portrays the college as the scene of a dispute between Henry Edward Manning and Dr Errington over whether a recusant or an ultramontane style should prevail there, and ultimately over who was to succeed Wiseman as second Cardinal Archbishop of Westminster.

[3] In 1869, Manning, now Archbishop, set up a seminary in Hammersmith, and for the first time St Edmund's ceased to be a theological college.

In 1874, the junior boys were separated from the rest of the college into St Hugh's Preparatory School, in a house originally built by Pugin for the Oxford convert William George Ward.

Numbers in the school increased significantly, and in 1904 Archbishop Francis Bourne decided to return the seminarians to the college.

In 1996, an infants' department was added to the junior school, meaning that St Edmund's would now educate pupils aged 3–18.