Pembina, a screw gunboat built by Thomas Stack and Novelty Iron Works, New York City, was commissioned 16 October 1861.

By the end of the month, she had engaged Confederate positions at Port Royal Ferry and into January 1862 assisted in clearing the Coosaw River.

In May, she shifted to the Carolina coast for operations in the Stono River, where on 6 June seized her first prize, the schooner Rowena.

Later shifted to the U.S. Gulf Coast, she captured a second vessel, the sloop Elias Beckwith, near Mobile, Alabama, 23 April 1863.

Remaining on the Gulf Coast, she seized her third and last blockade runner, the Dutch brig Geziena Hilligonda, carrying medicines, iron and cloth, off Brazos Santiago, Texas, on 4 December 1864.