In addition to boosting the morale of Americans citizens, the Doolittle raid had a significant impact on the course of the War in the Pacific. At the time of the raid, the Japanese Naval General Staff and the Combined Fleet were engaged in a fierce debate over what Japan's next move should be. The General Staff members were in favor of capturing more of New Guinea and obtaining additional footholds in the Solomons and in New Caledonia; the Japanese could then use these positions to menace Australia. On the other hand, Admiral Yamamoto, Commander of the Combined Fleet, argued that a strategic victory over the United States was more important than further territorial gains, and he spoke in favor of forcing a showdown with the American carriers by attacking Midway Island, the key defensive island for Hawaii; Yamamoto believed that the Americans would be forced to defend the island, and that Japan, with its numerically superior carrier fleet, would then force America out of the Pacific.

This debate was still raging at the time of the Doolittle raid. The attack came as quite a shock to the Japanese military leaders, and while the American bombs did little important damage to Tokyo, the ability of the Americans to attack the Japanese capital was a threat to Japan's emperor - a man revered by the Japanese as a god. Midway Island was the hole in the Japanese defensive perimeter through which Hornet was able to get close enough to Tokyo to launch its bombers, and so the Doolittle raid quickly ended the debate in the Japanese military. No Japanese general could countenance a plan that would leave open this hole in the Japanese defense, since doing so would imply a lack of concern for the safety of the emperor, and so the decision to attack Midway Island was quickly reached. Midway would be the turning point in the war for the Americans; their victory over the Japanese would start them on the path to winning the war.