 "Shōkaku" was 10,000 tons heavier than , mainly due to the extra armor incorporated into the ship's design.Vertical protection consisted of on the main armor deck over the machinery, magazines and aviation fuel tanks while horizontal protection consisted of along the waterline belt abreast the machinery spaces reducing to outboard of the magazines

Unlike British carriers, whose aviation fuel was stored in separate cylinders or coffer-dams surrounded by seawater, all pre-war Japanese carriers had their aviation fuel tanks built integral with the ship's hull and "Shōkaku" was no exception.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.