Linscott was appointed Operations and training officer on the staff of Amphibious Force, Atlantic Fleet under Major General Holland Smith and promoted to the rank of colonel in October 1941. Following the entry of the United States into the World War II, Linscott was ordered for duty to the South Pacific in June 1942 and attached to the staff of commander, Amphibious Force South Pacific under Vice Admiral Richmond K. Turner. Linscott was appointed assistant chief of staff and took part in several major campaigns in the Solomon Islands, New Georgia, Bougainville and the Gilbert and Marshall Islands. He remained on Turner's staff following the redesignation of Amphibious Force South Pacific to the Third Amphibious Force and distinguished himself in that capacity. He later received two awards of the Legion of Merit for his service.