On 7 December 1941, Lieutenant (jg) Fujita participated in the Attack on Pearl Harbor, where he was assigned as a section leader ("Shōtaichō") of fighter escort in the second wave. while strafing Kaneohe Airfield, his unit commander ("Buntaichō"), Lieutenant Fusata Iida, was shot down by anti-aircraft fire and Fujita took command over the remaining fighters and headed for Point Kaena, which was the rendezvous for the return to the carriers. On the way, they encountered a formation of Curtiss P-36 Hawk fighters and in the ensuing dogfight Fujita claimed to shoot down one of them. However, his own fighter was hit and he barely made it back to the carriers. Upon returning to Japan, he was promoted to full Lieutenant. In February 1942, he participated in the Bombing of Darwin. During the Indian Ocean Raid on 5 April, he and Petty Officer Kaname Harada attacked six British Fairey Fulmar and each claimed one of them shot down.