Malik was educated at the American Mission School for Boys, now Tripoli Evangelical School for Girls and Boys in Tripoli
Malik was educated at and the American University of Beirut, where he graduated with a degree in mathematics and physics. He moved on to Cairo in 1929, where he developed an interest in philosophy, which he proceeded to study at Harvard (under Alfred North Whitehead) and in Freiburg, Germany under Martin Heidegger in 1932. His stay in Germany, however, was short-lived. He found the policies of the Nazis unfavorable, and left soon after they came to power in 1933. In 1937, he received his Ph.D. in philosophy (based on the metaphysics in the philosophies of Whitehead and Heidegger) from Harvard University. He taught there as well as at other universities in the United States. After returning to Lebanon, Malik founded the Philosophy department at the American University of Beirut, as well as a cultural studies program (the 'civilization sequence program').