She was placed under the command of Lieutenant C. L. Franklin, USN, and spent her entire U.S. Navy service in the sounds and rivers of North Carolina.

On October 14, 1862, she was detailed to the blockade of Bogue Inlet, and a week later, captured and burned the schooner Adelaide with a valuable cargo of turpentine, cotton, and tobacco.

In November 1862, Ellis, under command of Lieutenant William B. Cushing, sailed up New River Inlet to capture Jacksonville, North Carolina.

After dark, her commanding officer moved all the crew except six and all her equipment and supplies except her pivot gun, some ammunition, two tons of coal, and a few small arms to one of the captured schooners.

Early on the morning of November 25, 1862, the Confederates opened fire on Ellis, and in a short time, Cushing was forced to decide between surrender and a pull of a mile and a half to a waiting schooner.