For the first 18 months of the Second World War, No. 31 Squadron remained stationed at the North-West Frontier. In April 1941, the Squadron started to be equipped with Douglas DC-2s and began flying support missions to RAF Habbaniya during the 1941 Iraqi coup d'état and the following Anglo-Iraqi War. Returning to India the squadron re-equipped with the Douglas Dakota Mk.I. After the Japanese invasion of Burma, it flew missions between Calcutta and Rangoon dropping supplies for the XIVth Army. After World War II the squadron moved to Java. In 1946, the Squadron was disbanded in Java and reformed at PAF Base Masroor, Mauripur Karachi, at that time in British India.