Upon the independence of Pakistan, Chaudhry got involved in the new government, moving up to high ranking positions in the National Assembly. He would end up joining the Pakistan Peoples Party and would be made President in 1973, when the head of the PPP, Zulfiqar Ali Bhutto was made Prime Minister.

Chaudhry was largely a figurehead, and was the first President with less power than the Prime Minister. This was due to the new constitution of 1973 that gave power to the Prime Minister. Previously, the President had been the chief leader of Pakistan, having the power to appoint Prime Ministers.

Fazal Ilahi Chaudhry would remian Prime Minister until 1978, when he would resign after the military took control of the government under General Muhammad Zia ul-Haq. Chaudhry would die on June 2, 1982.