The trio are accused of a total of 53 sex abuse offences at Swaylands School in Penshurst, Kent, between 1967 and 1993.
Kent Police said Colwyn Baker, 70, of Morningside, Edinburgh, faces 29 counts of indecent assault and five charges of buggery.
David Hennessy, 73, of Westfields, Narborough, King's Lynn, Norfolk, has been charged with 16 counts of indecent assault.
And a third man, 61-year-old Nigel Putman, of Kings Road, Slough, Berkshire, is accused of three counts of indecent assault.
A police spokesman said: "These charges follow a lengthy and complex investigation."
Swaylands School was set up in 1942, and between the mid 1960s and 1994 was operated and managed by the London Borough of Barnet.
Pupils aged between seven to 19 with learning, emotional and behavioural difficulties were placed there by local authorities across London and the South East.
All three men will appear at Maidstone Magistrates' Court on March 11 following an investigation by the Kent and Essex Serious Crime Directorate.