She was outfitted by the Union Navy as a gunboat to patrol navigable waterways of the Confederacy to prevent the South from trading with other countries.

The establishment of the Union blockade required small, fast, shallow-draft vessels like the Samuel Rotan for littoral operations.

She was fitted out as a gunboat at the Philadelphia Navy Yard; and commissioned there on 12 November 1861, Acting Master (equivalent to modern Lieutenant Junior grade) John A. Rogers in command.

Assigned to the Gulf Blockading Squadron, the schooner arrived off Fort Pickens, Florida, on 16 December 1861 and sent to Ship Island, Mississippi.

On 23 Jan 1862, she captured Confederate privateer, Calhoun, by forcing her to run aground in East Bay, formed by the Southwest-Pass and Grand-Pass fingers of the Mississippi delta.

The prize had been attempting to slip into the Southwest Pass laden with over 25 tons of gunpowder, rifles, chemicals, coffee, and other assorted cargo needed by the Confederacy.

Acting Volunteer Lieutenant W.W Kennison was given command on July 6 after heroic action as a gun captain when the USS Cumberland was sunk by the ironclad in Hampton Roads that previous March.

On the morning of 24 April, she and USS Western World captured schooners, Martha Ann and A. Carson, off Horn Harbor, Virginia.

On 24 July, Lt Commander Gillis reported "the blockade running in Mobjack Bay has been effectively stopped by placing the schooner Samuel Rowan at the mouth of the York River."

On the 27th, her picket boat seized a canoe which had run the blockade from the Severn River, Virginia, laden with corn, chickens, and eggs.