The 3rd Marine Division was officially activated on 16 September 1942 at Camp Elliott, San Diego, California. Most of the original members of the division were drawn from the cadre staff of the 2nd Marine Division. The division was initially built around the 9th Marine Regiment, commanded by Colonel Lemuel C. Shepherd, Jr. who later became the 20th Commandant of the Marine Corps. Major General Charles D. Barrett was the first commanding general of the division.

The division deployed into Auckland, New Zealand, between January and March 1943. In June of that year, it moved onto Guadalcanal for additional training. 1 November 1943 saw the division land as part of the Battle of Bougainville and fight on the island until their last unit to arrive, the 21st Marine Regiment, embarked on 9 January 1944. During the course of the battle the division had about 400 Marines killed.

The division returned to Guadalcanal in January 1944 to rest, refit, and retrain. The next operation in which the division took part was the Battle of Guam. From 21 July 1944 until the last day of organized fighting on 10 August, the division fought through the jungles on the island of Guam. During these 21 days of fighting, the division captured over 60 square miles (160 km²) of territory and killed over 5,000 enemy soldiers. The next two months saw continuous mopping up operations in which the Marines continued to engage leftover Japanese forces. At the end of the battle the division had sustained 677 Marines killed, 3,626 wounded, and nine missing.

The division remained on the island of Guam for training, until it embarked as part of the landing force for the Battle of Iwo Jima. The 3rd Marine Division was initially in reserve for the battle.^[6] However, the division was committed one regiment at a time when the initial regiments that landed there needed to be relieved.

The 21st Marines came ashore on 20 February followed by the 9th Marines, and then were reinforced by a battalion from the 3rd Marines on 25 February. The Marines of these two infantry regiments, supported by the artillery of the 12th Marine Regiment and tanks of the 3rd Tank Battalion, fought on Iwo Jima until the end of organized resistance on 16 March and the subsequent mopping up operations for the next month. All elements of the division were back on Guam by 17 April 1945. The fighting on Iwo Jima cost the 3rd Marine Division 1,131 killed in action and another 4,438 wounded.

After the return to Guam, the division began preparing for the invasion of Japan. This invasion never took place since Japan surrendered on 14 August 1945. The 3rd Marine Division was deactivated on 28 December 1945.

During the war, the 3rd Marine Division had three Seabee Battalions assigned to it. The 25th Naval Construction Battalion (NCB) was posted to 19th Marines as the third battalion of the regiment. These landed on Bougainville, as did the 71st NCB which was assigned as the 3rd Division's shore party there.

The 25th NCB also landed during the assault on Guam as the shore party to the 3rd Marine Regiment, after which the 19th Marines were deactivated, and the 25th NCB was reassigned. The 62nd NCB was then posted TAD to the 3rd for Iwo Jima. They were in the reserve, but they became the lead battalion in getting airfield No. 1 operational, after of the many casualties taken by the primary assault Seabees, the 133rd NCB.^{[citation needed]}