Fletcher was nominated for governor of Missouri by the National Union Party and elected in 1864. He served from 1865 to 1869, and on January 11, 1865, issued a "Proclamation of Freedom," adding his own imprimatur to the ordinance passed the same day by the state constitutional convention, abolishing slavery in Missouri. His administration was confronted with many problems, including amnesty for former Confederate soldiers, the disposition of the railroad property the state had acquired through default by the railroad companies failure to pay interest on bonds guaranteed by the state, and the reorganization of public education. The railroad property was sold under a guarantee of early completion and the state debt materially reduced. The public-school system was thoroughly reorganized and progress was made toward free education for all children.