In September 1861 New Era was purchased by the United States Army for use in its Western Gunboat Flotilla and was modified into a 355-ton timberclad gunboat. In November 1861 USS New Era took part in an expedition up the Cumberland River. Shortly thereafter she was renamed USS Essex and received an upgrade to iron armor and various other alterations. On 11 January 1862, USS Essex engaged Confederate States Navy gunboats near Lucas Bend, Missouri. On 6 February 1862, she took part in the attack on Fort Henry, Tennessee and was badly damaged by Confederate gunfire.