She was damaged by a dud aerial torpedo during an air raid at Rabaul on 5 November 1943, with one dead and nine wounded. The ship participated in the Battle of Philippine Sea.
In the Battle of Leyte Gulf, Fujinami escorted the 1st Diversion Attack Force, commanded by Admiral Kurita Takeo. She sustained minor damage from the air attacks on 24–25 October due to near-misses and strafing.
In the Battle off Samar on 25 October Fujinami was detached to assist, then she removed survivors and scuttled the cruiser with a torpedo. Some US survivors of the escort carrier have stated that the commanding officer Cmdr. Tatsuji Matsuzaki restrained his men from firing on them as they floated by Fujinami and was allegedly seen to salute the American sailors.
On 27 October, while steaming to assist the destroyer, Fujinami was sunk by aircraft from the aircraft carrier, 80miles north of Iloilo (12°N 152°W). She was lost with all hands, including the Chōkai survivors. The commanding officer was Cmdr. Tatsuji Matsuzaki from 31 July 1943 – 27 October 1944 (KIA).