Serious difficulties in the transaction of public business soon appeared throughout Fairfax County, where patrolling and skirmishing outside the ring of permanent fortified positions were daily occurrences. This was recognized in an ordinance adopted by the Secession Convention providing that when the court of any county failed to meet for the transaction of business or the public was prevented from attending the court "by reason of the public enemy", the court of the adjoining county where such obstructions did not exist had jurisdiction of all matters referrable to the court or the clerk of the court where normal business had ceased.[85]

As Virginia armed, troops of the Confederacy placed themselves in positions to repel invaders, and in May 1861, a company of the Warrenton Rifles established a camp at Fairfax Court House. On the morning of June 1, 1861, a body of Union cavalry rode through the town, and in the confused exchange of fire which followed, a Captain of the Rifles, John Quincy Marr, became the first officer casualty of the war.[86]

A month later, the tide of Union forces under McDowell swept past the courthouse on the way to its rendezvous at Bull Run, and back again to the safety of the fortified positions along the Potomac. In the wake of their victory at Bull Run, troops of the Confederacy established an outpost at Fairfax Court House to watch for signs that the Union Army might resume the offensive by moving against the Confederate earthworks near Centreville.

This outpost did not see any fighting for the time being, but it provided the site for what later was regarded as one of the decisive moments of the war. In September 1861, General Beauregard had established his headquarters at Fairfax Court House, and urgently pressed the newly-formed government of Confederate President Jefferson Davis for reinforcements with which to sweep into Pennsylvania and Maryland and, hopefully, to carry the Federal capital itself. A meeting was arranged at Beauregard's headquarters in which Davis, Generals Beauregard and J. J. Johnston, and certain of their trusted staff officers considered this plan. Their decision was to adopt a defensive posture and protect the borders of Virginia rather than take the offensive and invade the North. As events turned out, this decision had consequences of the greatest effect, for it was not until Lee marched out of the Valley on the road to Gettysburg in 1863 that there was another opportunity for the Confederacy to carry the war to the soil of the northern states.[87]

In the spring of 1862, the Confederate army retired from Fairfax Court House, and soon after that its line of fortifications at Centreville—the most extensive system of field fortifications in military history up to that time—was abandoned. As the Union armies took the initiative in their repeated efforts to reach Richmond, the crossroads at Fairfax Court House had key importance in the communication and supply systems of these forces.

From 1862 to the end of the war, Union troops remained in control of the crossroads and the courthouse. Contemporary photographs of the building show it being used as a lookout point and station for patrols. Other descriptions indicate that the courthouse was loopholed,[88] the furnishings were removed, and the interior generally was gutted so that only the walls and roof remained.[89] For all practical purposes, the courthouse and its related buildings were, in the years 1863 and 1864, a military outpost and minor headquarters in the Union army's system to protect its supply and communications lines from the irregular troops who kept hostilities constantly smoldering in Northern Virginia. Throughout the western part of Fairfax County, and in Loudoun, Fauquier and Prince William Counties, lived many who gave the appearance of innocent farmers during the daylight hours, but who changed into Confederate uniforms at night and on weekends to ride against isolated outposts or supply points of the Union army or destroy vulnerable bridges and communications centers.

The operations of these guerilla bands kept thousands of Union troops pinned down on rear area security guard duty, and preoccupied the forces assigned to Fairfax Court House. The difficulty of their task under the circumstances that prevailed in Northern Virginia was dramatized in the famous Confederate raid on Fairfax Court House by men under the command of Col. John S. Mosby when, on the night of March 8, 1863, the Confederate commander with about 30 men captured and carried off 33 prisoners, including Union Brigadier General Edwin H. Stoughton, and a large number of horses and quantity of supplies. Throughout 1863, 1864 and the spring of 1865 hardly a night went by without some cries of alarm and shots being fired because of the activities of the Confederate irregulars. Yet they took a substantial toll from the wealth and welfare of the very people they claimed to represent, for the Union troops soon learned more efficiency in their rear area operations, and increased the restrictions on movement of civilian traffic. The transaction of personal business in normal ways became virtually impossible. The historian, Bruce Catton, has assessed the activities of the guerilla bands as follows:

The quality of these bands varied greatly. At the top was John S. Mosby's courageous soldiers led by a minor genius, highly effective in partisan warfare. Most of the groups, however, were about one degree better than plain outlaws, living for loot and excitement, doing no actual fighting if they could help it, and offering a secure refuge to any number of Confederate deserters and draft evaders.... The worst damage which this system did to the Confederacy, however, was that it put Yankee soldiers in a mood to be vengeful.[90]

During the years when normal business at the courthouse was suspended and the county officials who held authority from the General Assembly were dispersed, some of the county's records were removed from the courthouse for safekeeping, and some were not.[91] In either case they were subject to the risks of loss and damage. Some were carried off and in later years have been brought to light as the descendents of Union and Confederate soldiers have found them in places where they had been put for safekeeping.

The jail building ceased to be used for its original purpose, and, during the latter months of the war, the jail of Alexandria County (now Arlington County) was utilized for Fairfax County's prisoners.[92]