Upon commissioning, the ship was assigned to the Fourth Carrier Division of the 1st Air Fleet, together with , under the command of Rear Admiral Kakuji Kakuta. She was tasked to support Operation AL, an attack planned to seize several Aleutian Islands to provide advance warning in case of an American attack from the Aleutians down the Kurile Islands while the main body of the American fleet was occupied defending Midway. "Jun'yō" carried 18 A6M2 Zeros and 18 D3As for this operation. At dawn on 3 June, she launched 9 Zeros and a dozen D3As to attack Dutch Harbor on Unalaska Island. They had to turn back due to bad weather, although an American PBY Catalina reconnaissance aircraft was shot down by a Zero. A second airstrike was launched later in the day to attack a group of destroyers discovered by aircraft from the first attack, but they failed to find the targets. Another airstrike was launched on the following day by the two carriers that consisted of 15 Zeros, 11 D3As, and 6 B5Ns and successfully bombed Dutch Harbor. As the aircraft from "Jun'yō" were regrouping after the attack, they were attacked by 8 Curtiss P-40 fighters that shot down 2 Zeros and a pair of D3As while losing 2 of their own. Another D3A got lost and failed to make it back to the carrier. Shortly after the aircraft were launched, the Americans attacked the carriers, but failed to inflict any damage. A Martin B-26 Marauder bomber and a PBY were shot down by Zeros, and a Boeing B-17 Flying Fortress bomber was shot down by flak during the attack.