Decommissioned once again in 1836, while she underwent remodeling, she was refitted with a light spar deck and declared the flagship of the South Sea Surveying and Exploring Expedition to the Antarctic region.
Following survey operations and other scientific work along the west coast of South America and in the South Pacific during the rest of the year, in late 1839 Vincennes arrived at Sydney, Australia, her base for a pioneering cruise to Antarctica.