After Mississippi seceded from the Union in early 1861, Charles Clark was appointed brigadier general in the Mississippi 1st corps. He commanded engagements in Kentucky and under Leonidas Polk at the Battle of Shiloh. He was then promoted to the major general of Mississippi state troops in 1863 and led a division at the battle of Baton Rouge where he was wounded, captured, and imprisoned. Clark is one of three Mississippi governors to be imprisoned including John Quitman and Theodore Bilbo.

 

 After Clark was released from prison and after the battle of Vicksburg in 1863, many Mississippians wanted to end the war and negotiate peace with the Union. Clark ran for governor as an anti-peace candidate and won. He was Inaugurated as the governor of Mississippi on November 16, 1863 under the Confederacy on the steps of the Lowndes County Courthouse in Columbus, Mississippi.  Because it was not safe to return to Jackson, Major Charles Allen of Macon, Mississippi offered an empty girls school in the area that could house the legislature. He also offered his home to Clark and his family as the temporary governors mansion. The legislature moved in and began working from the girls school and the Calhoun Institute, one of the most elaborate education buildings of antebellum Mississippi.

 

Union soldiers surrounded the building on June 3, 1865 and placed Clark under arrest for war crimes. He was placed at fort Pulaski near Savannah, Georgia. President Andrew Jackson pardoned him on October 12, 1865 and he was free to return home to Doro in Mississippi. Clark served as chancellor for the fourth judicial district and served on the bench until his death on December 17th, 1877.