The school opened in Cambridge in 1875 as a Connexional School to meet demands for higher education and to enable the sons of Methodists to enter Oxford or Cambridge. The traditions established by its first headmaster, Dr W.F. Moulton - high academic standards, broad curriculum, pastoral care, sporting prowess and impressive building programmes - have always characterized the school. A school chapel in his memory was opened in 1906. His successors included Dr. W.T.A. Barber and Harry Bisseker. The foundation stone of the gymnasium was laid in 1907 by Sir Henry Campbell-Bannerman and in 1914 King George V opened the new library. In World War II the senior and junior schools wre evacuated to Pitlochrie and Ashburton respectively. From 1975 to 1986 the hedmaster was the outstanding mathematician Bertie Bellis, formerly a pupil at Kingswood School and under him a computer laboratory was provided in 1982. The Design Centre was opened by the Duke of Edinburgh in 1987 and a sports hall by the Duchess of Kent in 1995. From 1990 to 2004 the Headmaster was Dr. John C.A. Barrett.
W.H. Balgarnie, a master for 37 years, was immortalized by ex-pupil James Hilton in his novel Goodbye Mr Chips, though a similar claim has been made for Joseph Clark Isard, a former pupil at Queen's College, Taunton, who taught at The Leys for one year. Other former pupils include the authors J.G. Ballard and Malcolm Lowry, and Sir Donald Bailey OBE, inventor of 'the military 'bailey bridge'. In 1997, with its preparatory school St Faith's, The Leys had 880 boarding and day pupils of both sexes, aged 4-18.