She was laid down as a Type C2-S-AJ3 ship under a Maritime Commission contract (MC hull 1395) on 3 July 1944, at Wilmington, North Carolina, by the North Carolina Shipbuilding Company; launched on 6 September 1944; sponsored by Mrs. H. V. Mason; converted to an attack cargo ship by the Todd-Erie Shipyard of New York City; and commissioned at the New York Navy Yard.

Twice the operation was interrupted by fierce typhoons which whirled into Buckner Bay and forced the ships at anchor to get underway and make for the relative safety of the open sea.

Her next orders — to proceed to Pearl Harbor — were cancelled when the ship received news that the Japanese were entertaining thoughts of surrender in the aftermath of the explosions of two atomic bombs.

She rendezvoused with units of the 3rd Fleet off Honshū and entered Tokyo Bay on the 27th, anchoring off the bomb-scarred Yokosuka Naval Base on the 30th to commence offloading her men and equipment to support the occupation.

Shifting to Nagoya on 1 November, Waukesha embarked demobilized sailors, soldiers, and marines to transport them home in "Operation Magic Carpet."

The ship later made more Far Eastern cruises and called at Okinawa en route to Qingdao, China, where she arrived on 2 March 1946.

Remaining until 8 March, the attack cargo ship set course, via Okinawa, for San Diego, California, which she reached on 15 April 1946.