It existed until General E. Kirby Smith surrendered all Confederate troops west of the Mississippi River at New Orleans, May 26, 1865.

As the Civil War began, many leading citizens were hoping the state could remain neutral in the growing conflict.

At a meeting held at Planters' House in St. Louis, June 11, 1861, it became clear that leading Missourians would have to choose sides.

The secession government applied for and, on November 28, 1861, was granted admission to the Confederacy as its purported 12th state.

As a result of military operations, however, particularly the Battle of Pea Ridge in March 1862, the Confederate government of Missouri was not able to establish control over much of the state; its jurisdiction extended only as far as Confederate military strength could reach.