Yamafuku Maru was laid down in 1939 at the Sakurajima shipyard of Osaka Iron Works K.K. at the behest of shipping company, Yamashita Kisen K.K.[2] She was launched in March 1940 and completed 10 July 1940.[2] On 15 May 1941, she was requisitioned as an auxiliary transport by the Imperial Japanese Navy and attached to the Yokosuka Naval District under Captain Honda Torao Yokosuka with Yokosuka as her homeport.[2]
On 23 November 1943, she departed Yokosuka for Truk as part of convoy No. 3123 with auxiliary transports Shoko Maru and Tatsutagawa Maru, IJN transport Manju Maru, cargo ship Shiganoura Maru, destroyer Oite, and auxiliary gunboat Choan Maru No. 2 Go.[2] On 23/24 November, the convoy was unsuccessfully attacked 20 nautical miles (37 km; 23 mi) northwest of Hachijo-Jima by USS Snapper with all torpedoes missing.[2] On 28 November 1943, the convoy was again attacked, this time USS Pargo and USS Snook 500 nautical miles (930 km; 580 mi) northwest of Guam; the initial attack was unsuccessful.[2]Snook attacked again just before midnight and successfully hit and sank Yamafuku Maru with four torpedoes at (18°21′N140°08′E / 18.350°N 140.133°E / 18.350; 140.133) with 60 men lost.[2] On 5 January 1944, she was struck from the Navy List.[2]