On 20 June 1941 Grenadier participated in the search for USS O-9, which had failed to surface after a deep test dive, and was present two days later as memorial exercises were conducted over the spot where O-9 and her crew lay.

Grenadier's first war patrol from 4 February to 23 March 1942 took her near the Japanese home islands, off the coast of Honshū, and brought her several targets but no sinkings.

Post-war examination of Japanese records showed Taiyō Maru to be more than just the ordinary transport; she was en route to the East Indies with a group of Japanese scientists, economists, and industrial experts, including renowned hydraulic engineer Yoichi Hatta who designed Chianan Irrigation and built Wusanto Reservoir in Taiwan, bent on expediting the exploitation of the conquered territory.

On 1 May 1942, Grenadier mistakenly sank the Soviet merchant ship Angarstroi in the East China Sea about 90 nautical miles (170 km; 100 mi) west-southwest of Nagasaki, Japan.

During the severe depth charging which followed, sea water seeped into the batteries; Grenadier's crew suffered headaches and nausea from chlorine gas poisoning for the remainder of the patrol.

[9][10] To increase the misery, on 20 November Grenadier spotted a Ryūjō-class aircraft carrier, escorted by a cruiser and a destroyer, heading through the Strait of Makassar too distant to shoot.

The submarine departed Australia on 20 March on her last war patrol and headed for the Strait of Malacca, gateway between the Pacific and Indian Oceans.

Fitzgerald "didn't think it advisable to make a stationary dive in 280 feet (85 m) of water without power," and the crew began burning confidential documents prior to abandoning ship.

Choko Maru picked up eight officers and 68 enlisted men[12] and took them to Penang, Malay States, where they were questioned, beaten, and starved before being sent to other prison camps.

A sunken wreck identified as the Grenadier was found by a team of four divers—Jean Luc Rivoire, Lance Horowitz, Benoit Laborie and Ben Reymenants—sitting upright under about 260 feet (79 m) of water and partly covered in fishing nets.

[13] The divers sent their findings to the Naval History and Heritage Command for verification; confirmation will place the wreck under the protections of the Sunken Military Craft Act.