With her sistership Zuikaku, Shokaku joined the Pearl Harbor attack fleet, and then participated in Japan's series of early wartime naval offensives, including an attack on Rabaul in January 1942, and the Battle of the Coral Sea in May. In the Indian Ocean raid of March 1942, she joined the aircraft carriers Akagi, Zuikaku, Soryu & Hiryu in raiding Columbo. There Adm. Nagumo succeeded in extensively damaging support facilities. That task completed, the task force sailed out and found/sank one British carrier; the Hermes, and two cruisers; the Cornwall & Dorsetshire, prior to moving on to the Coral Sea. Here she helped to sink USS Lexington, but was herself severely damaged by USS Yorktown's aircraft in return. After repairs, Shokaku took part in two further 1942 battles, both in concert with her sistership: the Battle of the Eastern Solomons, where they damaged USS Enterprise, and the Battle of Santa Cruz, where they sank USS Wasp but Shokaku was once again seriously damaged by dive bombers.
In 1943 she resumed her role as one of the Japanese Navy's most important fleet carriers, and was eventually sunk by the US submarine Cavalla (SS-244) on 19 June 1944, during the Battle of the Philippine Sea.