From ONI, Wilkinson was assigned briefly as Commander, Battleship Division 2, Pacific Fleet, in August 1942, then as Deputy Commander, South Pacific, under Admiral William Halsey and General Douglas MacArthur as theater commander beginning in January 1943.
Pursuing this strategy, Wilkinson earned the Distinguished Service Medal (DSM) for commanding the amphibious forces in the assaults on New Georgia, Vella Lavella, and the Treasury Islands; and established a key position on the west coast of Bougainville.