In July 1861, Confederate commander, responding to a Union offensive at Manassas Junction, hoped to move General from watchful Union forces near . Johnston marched south to Piedmont Station (present-day Delaplane) on the Manassas Gap Railroad, where his troops entrained to ride east to the battlefield near Bull Run—the first time in history that railroads were used to transport troops to a battlefield. At a crucial point on July 21, they smacked into Union general ‘s right flank, prompting a Union rout. Prior to this, the Manassas Gap Railroad had been involved in another memorable moment when Confederate general dismantled trains and rail on the at . He then directed them overland, pulled by horse teams some thirty-eight miles up the Valley Turnpike to the Manassas Gap’s depot at Strasburg. There, they were reassembled and moved for repair in .
In addition to its importance in moving troops and armaments, the Manassas Gap Railroad was important for moving meat—so much so, one historian has described it as “the Meat Line of the Confederacy.” Confederates erected a large meat-packing operation along its tracks at Thoroughfare Gap, with vast amounts of livestock coming from Valley farms. They were slaughtered, processed, and cured early in the conflict, and then transported to Confederate encampments. Moreover, the slaughterhouse was only thirteen miles west of the longer Orange and Alexandria line, carrying cars to far off locations. As the war progressed and Union forces moved in close proximity to the Manassas Gap Railroad, however, it and the packing plant were hastily abandoned and set to the torch.
This drew strong criticism from a variety of the Confederate decision-makers, notably involving the local commander Joseph Johnston, Subsistence Commissary Lucius Northrop, and finally Confederate president, all of them placing blame on the other. Union general Nathaniel P. Banks subsequently utilized the Manassas Gap Railroad, while Stonewall Jackson led attacks on the line and even created a temporary break. It eventually took the expertise of Union railroader Herman Haupt to thwart Jackson. Haupt supervised the rebuilding of the line from Rectortown to Piedmont, with Union forces in pursuit of Jackson. While under the stewardship of the gifted Haupt, the railroad was utilized by Union forces in the (1862) and (1863) campaigns, although it faced continuous threats from Confederates until the war’s end.