As his name suggests, he was of Huguenot (French Protestants who fled to South Africa and were assimilated in the Afrikaner population) descent.

Malan was educated at Paarl Boys' High, Victoria College, Stellenbosch, the University of the Cape of Good Hope (where he studied science) and Christ's College, Cambridge, graduating from Cambridge in 1894 with an LLB.

He never practised, however, and later that year became editor of Ons Land, the Cape's leading Dutch-language newspaper.

In 1908 he resigned from Ons Land and was appointed minister of agriculture in John X. Merriman's government.

He also acted as prime minister for eight months while Botha and Smuts were away at the Paris Peace Conference in 1919.