In November 1940, Yamaguchi was reassigned to command the 2nd Carrier Division, consisting of the aircraft carriers and . In preparation for the attack on Pearl Harbor, Yamaguchi trained his flight crews ruthlessly, which led to many accidents and complaints; however, the training paid off after the start of combat operations. Following the successful strike against the American fleet at Pearl Harbor, Yamaguchi′s carrier force participated in the Battle of Wake Island. After the start of 1942, he was sent south to assist in the Battle of Ambon in the Dutch East Indies, followed by the Bombing of Darwin in February. In March, his carriers supported Japanese forces in the Battle of Java, sweeping the Dutch East Indies of remaining Allied warships. In April, he crossed into the Indian Ocean to support the large-scale raid against the Royal Navy at and near Ceylon.