Company G of the 33rd Regiment of Virginia Infantry, part of the famous "Stonewall Brigade" under command of General Thomas "Stonewall" Jackson, was largely recruited in Mt. Jackson and vicinity.
The town saw conflict during the Civil War, incurred damage and was occupied by soldiers of both armies at various times. During his Valley Campaign of 1862, General Thomas "Stonewall" Jackson made one of his headquarters just south of town at a manor on Rude's Hill, about 3 miles south of Mt. Jackson. As a highly defensible high ground position, commanding the Valley Pike, the North Fork of the Shenandoah River and Meem's Bottom and approaches south, Rude's Hill had a particularly active role in the Civil War, occupied, encamped on and contested by both armies from 1862 to 1865.
On November 16–18, 1863 Col. William H. Boyd's Union cavalry reconnoitered from West Virginia to the area of the Valley Pike. The Federal troopers skirmished at Woodstock, Edinburg and Mt. Jackson. North of Mt. Jackson the Federals encountered Confederate cavalry under command of Maj. Robert White. White. The rebel troopers retreated through Mt. Jackson fighting, crossing the bridges through Meems Bottom and to the defensible position on Rude's Hill. Realizing that White's horse artillery could sweep the bridge from the hill, Boyd withdrew from the skirmish at Rude's Hill and withdrew to Woodstock, pursued by Confederate cavalry. Boyd's reconnaissance-in-force then returned to West Virginia. Losses from the Mount Jackson cavalry engagement were light on both sides.
Troop movements and engagements in and near the town were particularly active in May 1864, around the Battle of New Market, 7 miles from Mt. Jackson. On May 14 a delaying action was fought at Rude's Hill by the Confederate 18th Virginia Cavalry, under the overall command of Col. John Imboden. The Confederate cavalry slowed the Union advance, enabling Gen. John Breckinridge to gather the main body of his Confederate forces at New Market, about 4 miles away. After losing the battle on May 15, Union General Franz Sigel managed to organize a rearguard on Rude's Hill, with infantry east of the turnpike, some cavalry west of the road and the artillery behind the line. Due to the exhaustion of the men and low ammunition, Sigel decided to retreat across the Meems bottomland and the North Fork of the Shenandoah River to Mount Jackson. Breckinridge at the same time, concerned the Federals would make a stand on Rude's Hill, advanced his cavalry and artillery to the crest of Rude's Hill where they shelled and harassed Sigel's retreating Federals in Meems Bottom. The Union army managed to cross Mill Creek at Mt. Jackson and burned the bridge that spanned the creek to Mt. Jackson before the Confederates could catch up.
Rude's Hill was also the site of a Confederate stand following their demoralizing and humiliating defeat on September 22, 1864, at the Battle of Fisher's Hill, about 23 miles north of Mt. Jackson. Gen. Jubal Early rallied and deployed his remaining Confederate infantry in line across the top of the hill on November 22, 1864, to check the advance of two divisions of Union cavalry following them. The Union cavalry charged the Confederate line but were repulsed in a sharp action. Early then retreated from Rude's Hill to Harrisonburg, eventually retreating to the entrance of the Shenandoah Valley at Browns Gap in the Blue Ridge.
In a predawn raid on 3 Oct. 1864, Confederate Captain John McNeill led approximately 50 Confederate rangers against roughly 100 Union troopers of the 8th Ohio Cavalry Regiment guarding a bridge from Meems Bottom, a strategic crossing of the Valley Turnpike over the North Fork of the Shenandoah River to Mt. Jackson. The attack lasted just fifteen minutes with most of the Union cavalry captured but McNeill, one of the best-known and feared Confederate partisan raiders as leader of McNeill's Rangers, was mortally wounded. He was taken to the house on Rude's Hill, where his identity was later discovered by Union General Philip Sheridan's troops. He was later secreted away by a band of Confederates after the Federals had temporarily left, thinking him to sick to move. McNeill was taken by the Confederates to Harrisonburg where he died on November 10.
In October 1864, as part of Union General Phil Sheridan's 1864 Valley Campaign aimed at destroying anything of potential military value, Mt. Jackson's mill was obliterated. Towards the end of the war, Rude's Hill was also the scene of a cavalry skirmish when Confederate Brigadier General Thomas Rosser's troopers attacked Union troops guarding Confederate prisoners on March 7, 1865.
Outside of troop movements or significant engagements, Civil War skirmishes were recorded as happening at Mt. Jackson on March 25, 1862; June 3, 6 and 16, 1862; November 18, 1863; September 23–24, 1864; October 3, 1864; and March 7, 1865.
As the southern terminus of a north–south railroad line connecting to Northern Virginia, Mt. Jackson was an ideal location for military hospitals and became a center for military medical treatment, ultimately used by both sides in the conflict. A Confederate hospital was built in Mt. Jackson along the Manassas Gap Railroad in 1861, to which wounded and sick were to be transported by rail from the Confederate Army of Northern Virginia. Dr. Andrew Russell Meem, a graduate of Princeton University and a native of Mt. Jackson, ran the hospital and the land was donated by Col. Levi Rinker, a large slaveowner and one of the wealthiest families in the valley. The hospital, intended as a wayside hospital for intermediate care not a permanent treatment facility for badly wounded, consisted of three two story buildings and could accommodate 500 patients, a mixture of wounded soldiers and those sick from disease. The hospital functioned nearly continuously throughout the war, attending to wounded from the battles of Antietam, Gettysburg as well as the Shenandoah Valley campaigns. In addition, with shifting control of the town some Union soldiers were treated at the hospital and at other makeshift hospitals in the town, including Union Church. A Confederate cemetery was established across from the hospital, directly along the tracks of the railroad. At the end of the war in 1865, Union troops tore down the hospital, using the lumber to build a federal occupation installation on Rude's Hill, 3 miles south of Mt. Jackson. This post was removed in 1875 when the Reconstruction era ended. The Confederate cemetery is all that visibly remains of the hospital today in the town of Mt. Jackson.
The Union Army under General Fremont crossing the north fork of the Shenandoah at Mt. Jackson during the 1862 campaign.