After about an hour's flight, the Japanese aircraft carrier Hiryu's eighteen dive bombers approached the reported position of the U.S. carriers. They were detected by radar on USS Yorktown (CV-5) several minutes before noon on 4 June, and combat air patrol was vectored to intercept. Shortly thereafter, the Japanese flight commander, Lieutenant Michio Kobayashi spotted Yorktown. Defending F4F-4 "Wildcat" fighters shot down most of Kobayashi's Type 99 shipboard bombers (a type later called "Val" by the Allies). However, seven Japanese planes were able to carry out an effective dive bombing attack.

Three Japanese bombs hit Yorktown, and a near-miss astern caused casualties on the ship. One bomb, dropped by a plane that had been shot down, burst on impact with the flight deck, just aft of the midships elevator. It opened a hole about twelve feet in diameter and showered nearby gun positions with fragments, killing and wounding many Yorktown crewmen. It also started fires on the hangar deck below, but these were quickly extinguished.

Another bomb hit Yorktown's forward elevator, penetrated through several decks and exploded, causing a persistent fire but no serious damage. The third bomb, however, pierced the flight deck just to port of the island, blew holes in the boiler room uptakes, started a severe fire in the smokestack area and put most of the boilers out of action. This bomb's effects brought Yorktown to a stop.