Stuart was a member of the state house of representatives in 1842 and was elected as a Democrat from Michigan's 2nd congressional district to the 30th Congress to fill the vacancy caused by the death of Edward Bradley.

He resumed the practice of law in Kalamazoo and was a delegate to the 1860 Democratic National Convention from Michigan.

During the Civil War, Stuart raised and equipped the 13th Michigan Infantry, of which he was commissioned colonel.

Charles E. Stuart died in Kalamazoo and was interred in Mountain Home Cemetery.

His home in Kalamazoo at 427 Stuart Ave. is listed on the National Register of Historic Places.