During the Civil War the Stone House at Manassas Battlefield was involved in both "First Manassas" and "Second Manassas" as a sanctuary of sorts for wounded soldiers.

During the Civil War, the Stone House area witnessed significant action during the two battles of Manassas, as the adjacent roads became corridors for military movement and the tide of battle swept repeatedly over the crossroads.

At the First Battle of Manassas, on July 21, 1861, Confederate troops met a Union flanking force on Matthews Hill, one-half mile north of the Stone House. After a delaying action, the Southerners retreated past the Stone House to Henry Hill, where Confederate reinforcements gathered. The Stone House, meanwhile, fell into the hands of pursuing Union troops advancing south along the Sudley Road, and the building served as shelter for the wounded.

After repulsing the Union attack on Henry Hill and Chinn Ridge during the afternoon, Confederate troops retook the Stone House, capturing a large number of wounded and 36 other Federals inside. 　

During the Second Battle of Manassas (August 28-30, 1862), Union commander John Pope arrived on the field on August 29 and established his headquarters on Buck Hill, immediately north of the Stone House. On the afternoon of August 30, a massive Confederate counterattack drove Pope's army eastward to the Sudley Road corridor.

Along the Sudley Road and on Henry Hill to the south of the Stone House, Union forces held back the Confederate assault and staved off disaster. In its withdrawal from the battlefield, much of the defeated Union Army retreated past the Stone House along the Warrenton Turnpike. As in the first battle, the Stone House again sheltered Union wounded. After Second Manassas, Confederate forces used the building for paroling captured Federals.