At Pearl Harbor the vessel took on more Seabees, and departed on 27 April for Samar in the Philippine Islands via Eniwetok and Kossel Roads, disembarking her passengers at the destination on 17 May 1945.

By this time the Battle of Okinawa was drawing to a close, so Grafton departed Samar on 24 May to pick up a B-24 bomber service group in the Palaus and transport them to the newly conquerend Japanese island.

Over the next four nights, the US Naval assault fleet was subjected to heavy air attacks, which Grafton helped repel with her antiaircraft guns.

On 28 June Grafton took on board 1000 Japanese prisoners of war, and then sailed via Saipan to Pearl Harbor, where she offloaded them on 13 July.

Following the end of Magic Carpet, Grafton sailed for Norfolk, Virginia via the Panama Canal and San Francisco, arriving in Hampton Roads on 21 March 1946.