In June 1862, Jewett joined the Union Army to fight in the Civil War, and was commissioned as a second lieutenant in the 9th Vermont Infantry. On August 3, he was captured, and remained a prisoner of the Confederacy for 25 days. Jewett was promoted to first lieutenant in May 1863. During his service, he took part in the battles of Harper's Ferry (September 13 and 15, 1862), Newport Barracks (February 2, 1864), Chaffin's Farm (September 29, 1864), and Fair Oaks (October 27, 1864). He resigned in November 1864, and returned to Vermont.