He returned to Scots in 1956 and in 1959 he was appointed Deputy Headmaster at Toowoomba Grammar School.
In 1964 he moved to Trinity Grammar School, Summer Hill as a housemaster and later served as Senior Master from 1966 until 1968.
In Our Proper Concerns: A History of the Headmasters' Conference of the Independent Schools of Australia, Wilson Hogg says that, "His was an imaginative appointment.
Despite the fine qualities of such headmasters as Lawrence Pyke and Douglas Trathen, the school had been passing through a protracted period of uncertainty and difficulty ... a decade before Tony Rae's assumption of office no one would have suspected that Newington would emerge in the eighties as a leading school in the arts; notably in drama, and pre-eminently in music.
[2] On 26 January 1992, Rae was made a member of the Order of Australia for "service to education as headmaster of Newington College and through the Association of Independent Schools".