On her first war patrol, from 8 February to 4 April 1942, Grampus sank an 8636-ton tanker, the only kill of her short career, and reconnoitered Kwajalein and Wotje atolls, later the scene of bloody but successful landings. Grampus's second and third patrols were marred by a large number of antisubmarine patrol craft off Chuuk (Truk) and poor visibility, as heavy rains haunted her path along the Luzon and Mindoro coasts. Both patrols terminated at Fremantle, Australia.
Taking aboard four coast watchers, Grampus sailed on 2 October 1942 for her fourth war patrol. Despite the presence of Japanese destroyers, she landed the coast watchers on Vella Lavella and Choiseul islands while conducting her patrol. This patrol, during the height of the Guadalcanal campaign, took Grampus into waters teeming with Japanese men-of-war. She sighted a total of four enemy cruisers and 79 destroyers in five different convoys. Although she conducted a series of aggressive attacks on the Japanese ships, receiving 104 depth charges for her work, Grampus was not credited with sinking any ships. On 18 October 1942, Grampus even scored a direct hit on the Yura, but the torpedo failed to explode. She returned to Australia on 23 November.
Grampus's fifth war patrol, from 14 December 1942 to 19 January 1943, took her across access lanes frequented by Japanese submarines and other ships. Air and water patrol in this area was extremely heavy, and although she conducted several daring attacks on the 41 contacts she sighted, Grampus again was denied a kill.
In company with Grayback, Grampus departed Brisbane on 11 February 1943, for her sixth war patrol from which she failed to return; the manner of her loss still remains a mystery. Japanese seaplanes reported sinking a submarine on 18 February in Grampus's patrol area, but Grayback reported seeing Grampus in that same area 4 March. On 5 March 1943, the Japanese destroyers Minegumo and Murasame conducted an attack preceding the Battle of Blackett Strait, near Kolombangara island. A heavy oil slick was sighted there the following day, indicating that Grampus may have been lost there in a night attack or gun battle against the destroyers. The Japanese destroyers had by then already been sunk in a night action with U.S. cruisers and destroyers.
When repeated attempts failed to contact Grampus, the submarine was declared missing and presumed lost with all hands. Her name was struck from the Naval Vessel Register on 21 June 1943.