The initial Japanese attack wave hit the Pearl Harbor Navy Yard area relatively lightly, with a few torpedoes launched at ships along 1010 Dock and some dive bombers targeting that vicinity and the drydock area immediately to the southward. The torpedo planes made one hit, on the light cruiser Helena, opening two of her engineering spaces to the sea. The minelayer Oglala, tied up alongside Helena, fared much worse. This old converted passenger ship had her port side opened up by the blast of the torpedo that hit the cruiser, and the resulting inrush of water could not be controlled. About two hours later, Oglala rolled over to port and sank alongside 1010 Dock.

The second Japanese attack wave's horizontal and dive bombers gave the Navy Yard's drydock area considerable attention. Though their efforts were somewhat mitigated by the diversion of some planes against USS Nevada as she passed nearby, these bombers made several hits, wrecking three destroyers and damaging the battleship Pennsylvania. The latter, Flagship of the Pacific Fleet and one of the raiders' priority targets, was "high and dry" in Drydock # One with destroyers Cassin and Downes. One bomb hit Pennsylvania amidships, killing eighteen crewmembers and producing modest damage to the battleship. Other bombs, hitting on and near the two destroyers, opened their fuel tanks and set intense fires. Ammunition explosions, including the detonation of a torpedo on Downes, added to the destruction, which was compounded when the drydock was partially flooded. Cassin then lifted off her blocks and rolled over against Downes.

Dive bombers from the second wave also struck the destroyer Shaw, which was in the floating drydock YFD-2. The resulting fires spread to Shaw's forward magazines, which blew up spectacularly, severing her bow. However, the rest of the ship remained afloat as the drydock sank beneath her. The little tug Sotoyomo, also in YFD-2, was badly burned by Shaw's fires and went down, too.

Japanese bombs near-missed some of the ships at the piers in the northeastern part of the Navy Yard, producing notable damage to the hull of light cruiser Honolulu. However, the attackers' concentration on battleship targets left the Yard's vital industrial facilities essentially untouched. These were soon hard at work on rescue, repair and salvage jobs, of which there were many immediately at hand.