The son of a Unitarian minister, Holt attended Lord Williams's School in Thame, Oxfordshire, and studied history at University College, Oxford.
He then obtained a diploma of education and worked as a secondary school teacher in Anglo-Egyptian Sudan 1941–53 (initially at Gordon Memorial College, the country's leading school), and then as Government Archivist and part-time lecturer at the University College of Khartoum 1952–55.
[1] Holt completed a DPhil at Oxford on “The personal rule of the Khalifa Abdallahi al-Ta'aishi”, on the second ruler of the Sudanese Mahdist State (1885-1899), initially under the supervision of H.A.R.
A Study of its Origins, Development, and Overthrow (1958) was based on his DPhil thesis, and was followed by A modern history of the Sudan, from the Funj Sultanate to the present day (1965, later republished as The history of the Sudan from the coming of Islam to the present day).
Holt was also one of the founding editors of The Cambridge History of Islam, along with Ann K. S. Lambton and Bernard Lewis.