For the 18 months following her second commissioning, Rapidan carried fuel from the Texas oil ports to ships and stations in the Caribbean and along the U.S. Atlantic coast.

Between September 1941 and November 1942, she supplied petroleum products to Atlantic Fleet units at Halifax, Canada, Naval Station Argentia, Newfoundland, Reykjavík and Hvalfjörður in Iceland, and various ports in Greenland.

Repairs were completed at Charleston; and, on the 25th, she resumed her oil runs, operating as far south as the Netherlands West Indies, and as far north as Argentia.

Transiting the Panama Canal on 19 March, she steamed up the west coast to Seattle, whence she carried her liquid cargo to Kodiak, Cold Bay, Dutch Harbor, and other Aleutian ports.

In 2006, a horse racing track in Monticello, New York was the site of the so-called miracle, in which a racehorse hit veteran Don Karkos in the exact spot where he had been injured by shrapnel and lost sight in one of his eyes during his time on USS Rapidan.