On 6 October 1941, Yanagimoto was given command of the aircraft carrier , on which he participated in the attack on Pearl Harbor in the opening stages of the Pacific War. He was subsequently at the Battle of Wake Island and the Indian Ocean raids. Yanagimoto chose to go down with his ship when "Sōryū" was sunk by United States Navy aircraft at the Battle of Midway, despite the efforts of his crew to convince him to leave the burning bridge. He was posthumously promoted to the rank of rear admiral and awarded the Order of the Rising Sun, 2nd class.