She was launched on November 17, 1860 and was named after Captain Thomas Freeborn, who lost his life in the discharge of his duty on board the ship John Minturn on December 15, 1846.
[1] Thomas Freeborn was one of three steam tugs chartered by the Navy in April 1861 for use in the unsuccessful Fort Sumter relief expedition.
The next day, Thomas Freeborn carried Senators Benjamin F. Wade, Zachariah Chandler, and Robert Morrill to Washington, returning to Hampton Roads on 22 May.
On 24 June, Thomas Freeborn and USS Pawnee shelled Confederate installations at Mathias Point, Virginia, after having received sporadic shore fire from the batteries earlier.
On 21 February 1863, USS Dragon and Thomas Freeborn engaged a Confederate battery near Fort Lowry, Virginia; each vessel received minor damage.
Finding nothing, she was ordered to proceed to Cherrystone, Virginia, on 1 May 1865 and warned of the expected arrival of Confederate ram CSS Stonewall from Europe.
Thomas Freeborn was decommissioned at the Washington Navy Yard on 17 June 1865 and was sold at auction there on 20 July to Anthony Raybold.