Upon commissioning, I-364 was attached formally to the Yokosuka Naval District and was assigned to Submarine Squadron 11 for workups.[2] With her workups complete, she was reassigned to Submarine Squadron 7 on 6 September 1944.[2] On 14 September 1944, she departed Yokosuka bound for Wake Island on her first transport mission, expecting to reach Wake in late September.[2]
I-364 was on the surface in the Pacific Ocean 250 nautical miles (460 km; 290 mi) east of Honshu′s Boso Peninsula on a base course of 90 degrees (i.e., due east) and making 9.5 knots (17.6 km/h; 10.9 mph) when the United States Navy submarine USS Sea Devil (SS-400) detected her on radar at 04:32 on 16 September 1944.[2]Sea Devil began to track I-364, and Sea Devil′s commanding officer observed a large Rising Sun insignia painted on I-364′s conning tower and misidentified her as an "I-58-class" submarine.[2] At dawn, I-364 began to zigzag and Sea Devil began an approach for an attack position.[2] As I-364 passed in front of Sea Devil at a range of 1,800 yards (1,600 m), Sea Devil fired four Mark 18 Mod 2 electric torpedoes.[2] Two of them hit, and I-364 sank with the loss of her entire crew of 77 at 34°30′N145°23′E / 34.500°N 145.383°E / 34.500; 145.383 (I-364), leaving behind a large pall of brown smoke.[2]
On 31 October 1944, the Imperial Japanese Navy declared I-364 to be presumed lost with all hands.[2] She was stricken from the Navy list on 10 December 1944.[2]