At the beginning of the Civil War, Jouett was captured by Confederates at Pensacola, Florida, but was soon paroled.

He then joined the blockading forces off Galveston, Texas, distinguishing himself during the night of 7/8 November 1861 in the capture and destruction of Confederate schooner Royal Yacht, while serving on USS Santee.

Metacomet was sent after two Confederate gunboats, and in a short chase Jouett riddled the Gaines and captured the Selma.

Admiral Jouett was named President of the Board of Inspection and Survey and served from June 1886 to February 1890.

A special act of Congress granted him full pay for the rest of his life as a reward for his brilliant service.