Her enhanced protection compared favorably to that of contemporary Allied aircraft carriers and enabled Shōkaku to survive serious damage during the battles of the Coral Sea and Santa Cruz.

The dangers this posed, however, did not become evident until wartime experience demonstrated these were often prone to cracking and leaking as the shocks and stresses of hits or near-misses to the carrier's hull were inevitably transferred to and absorbed by the fuel tanks.

Following the debacle at Midway in mid-1942, the empty air spaces around Shōkaku's aviation fuel tanks, normally pumped full of inert carbon dioxide, were instead filled with concrete in an attempt to protect them from possible damage.

In spite of all the additional armor, greater displacement and a 2.1 m (6.9 ft) increase in draught, Shōkaku was able to attain a speed of just over 34.2 kn (63.3 km/h; 39.4 mph) during trials.

Two same-sized downward-curving funnels on the ship's starboard side, just abaft the island, vented exhaust gases horizontally from the boilers and were sufficiently angled to keep the flight deck free of smoke in most wind conditions.

[4] In September 1942, a Type 21 air-warning radar was installed on Shōkaku's island atop the central fire control director, the first such device to be fitted on any Japanese carrier.

Shōkaku and Zuikaku joined the Kido Butai ("Mobile Unit/Force", the Combined Fleet's main carrier battle group) and participated in Japan's early wartime naval offensives, including Pearl Harbor and the attack on Rabaul in January 1942.

In the Indian Ocean raid of March–April 1942, aircraft from Shōkaku, along with the rest of Kido Butai, attacked Colombo, Ceylon on 5 April, sinking two ships in harbor and severely damaging support facilities.

During this operation, Shōkaku's aircraft helped sink the American aircraft carrier USS Lexington during the Battle of the Coral Sea but was herself seriously damaged on 8 May 1942 by dive bombers from USS Yorktown and Lexington which scored three bomb hits: one on the carrier's port bow, one to starboard at the forward end of the flight deck and one just abaft the island.

On the journey back, maintaining a high speed in order to avoid a cordon of American submarines out hunting for her, the carrier shipped so much water through her damaged bow that she nearly capsized in heavy seas.

The Type 21 radar, installed a month ago, enabled the early detection of the incoming U.S. planes, so refueling crews were alerted below deck, giving them time to drain and purge the aviation gasoline lines before they were ruptured by bomb hits, thus saving the ship from the catastrophic avgas fires and explosions that caused most of the carrier sinkings in the Pacific theater.

After several months of repairs and training, Shōkaku, now under the command of Captain Hiroshi Matsubara, was assigned in May 1943 to a counterattack against the Aleutian Islands, but the operation was cancelled after the Allied victory at Attu.

On 15 June, she departed with the Mobile Fleet for Operation "A-Go", a counterattack against Allied forces in the Mariana Islands, resulting in the Battle of the Philippine Sea.

Her strike waves suffered heavy losses from U.S. combat air patrols and anti-aircraft fire, but some survived and returned safely to the carrier.

As Shōkaku had been in the process of refueling and rearming aircraft and was in an extremely vulnerable condition, the torpedo hits started avgas fires that proved impossible to control.

The order to abandon ship was given, but before the evacuation had progressed very far, Shōkaku abruptly took on water forward and sank quickly bow-first at position 11°40′N 137°40′E / 11.667°N 137.667°E / 11.667; 137.667, taking 1,272 men with her.