Yamaguchi returned to Japan briefly in late April for maintenance on his fleet. In June 1942, he was assigned to the Midway operation. During the battle, on 6 June 1942, Yamaguchi disagreed with the fleet commander, Vice Admiral Chūichi Nagumo. A reconnaissance plane discovered an American aircraft carrier () near Midway. At that moment, the Japanese planes had been armed for a second strike on Midway, with the "Kate" level bombers carrying bombs rather than torpedos. Yamaguchi called for an immediate strike on the US ship, with the planes armed as they were, but Nagumo decided instead to wait until the planes had been re-armed. Shortly afterward, American carrier aircraft destroyed all the Japanese carriers except Yamaguchi′s flagship "Hiryū". Yamaguchi quickly ordered two successive attacks on "Yorktown" which crippled it. "Hiryū" was then destroyed by aircraft from , plus some orphaned "Yorktown" aircraft.