With the outbreak of the Civil War, Munford was mustered into the Confederate States Army on May 8, 1861 by Colonel Jubal A. Early and served as a lieutenant colonel with the 30th Virginia Volunteer Regiment, a mounted infantry regiment, which fought at the First Battle of Manassas. When the cavalry was reorganized under J.E.B. Stuart, he was promoted to colonel of the 2nd Virginia Cavalry as the 30th Virginia Volunteer Regiment had been redesignated. In the 1862 Shenandoah Valley Campaign, Munford served under Thomas J. "Stonewall" Jackson as commander of a cavalry brigade of two regiments, succeeded Colonel and acting Brigadier General Turner Ashby as commander of all of Jackson's cavalry, upon that officer's death, and fought well at the Battle of Cross Keys and captured many prisoners at Harrisonburg, Virginia. During the Peninsula Campaign, he led his men at the Battle of White Oak Swamp. He served with efficiency in the Second Manassas Campaign in which he was slightly wounded at Turkey Run Bridge and the Second Battle of Bull Run. Munford was temporarily given an independent command of Robertson's brigade in the Maryland Campaign. During that campaign he successfully cleared Leesburg, Virginia of Union forces at the Battle of Mile Hill so that the army could cross the Potomac River from there. He led his troops in a key defensive position protecting Crampton's Gap at the Battle of South Mountain. His men saw limited action at the Battle of Antietam. They participated in several of Stuart's cavalry battles during the 1863 Gettysburg Campaign and the Bristoe Campaign, as well as in cavalry actions in the Overland Campaign in Spring 1864 under Major General Fitzhugh Lee.