On May 18, 1836, Congress passed an amendment to the Naval Appropriations Bill authorizing the President to "send out a surveying and exploring expedition to the Pacific Ocean and the South Seas," and a total of $300,000 was appropriated for the expedition. The amendment passed the Senate by a vote of 26 to 3 while in the House there was considerable opposition where the final vote was 79 to 65.

The primary purpose of the expedition was to aid commerce and navigation, but it was also supposed "to extend the bounds of science and to promote knowledge". In April 1838, four naval vessels were assigned to the expedition, with the Vincennes, a sloop of war of 780 tons, designated as the flagship. Other vessels were the Peacock, a sloop of war of 650 tons, the Porpoise, a brig of 230 tons, and the store ship Relief. Two New York pilot boats, the 110-ton schooner Sea Gull and the 96-ton schooner Flying Fish were purchased for the expedition to be used as survey vessels close in to shore.

Wilkes was not the navy's first choice to lead the expedition. Thomas Ap Catesby Jones was originally placed in command but resigned in disgust due to delays coming from the Secretary of the Navy. The command was then offered to Commodore Shubrick, who declined. Captains Kearney and Gregory were asked and they thought it politically incorrect and so stepped aside. The next man chosen was Charles Wilkes. 

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