1861
May 23 The State of Virginia ratified the Articles of Secession from the United States.
June 1 Joseph Johnston evacuated Harpers Ferry and pulled his Army of the Valley back to Winchester. Winchester became the front line of the Confederacy.
July 18 Johnston marched his Valley Army from Winchester to reinforce Beauregard at Manassas, leaving a small force of militia behind to defend the town. But Union forces under Patterson withdrew across the Potomac, leaving Winchester in Confederate hands.
November 4 Thomas ‘Stonewall’ Jackson was assigned to the command of the Valley District, with headquarters at Winchester. He took residence in a house on North Braddock Street, sending for Mrs. Jackson. It was his headquarters and home until March of 1862, when he was forced to evecuate Winchester and withdraw up the valley. Today his headquarters is a museum.
1862
March 11 Jackson evacuated Winchester in the face of superior Union forces.
March 12 Union troops under Nathaniel Banks occupied Winchester for the first time.
March 23 First Battle of Kernstown

Thomas Jackson (4,000) vs. Nathan Kimball (9,000)

Jackson responded to intelligence that most Union troops had left the city by attackeding what he hoped was a small rearguard. His information was wrong. Jackson’s only defeat while in command of an army forced him to retreat back up the Valley. It was the only battle Jackson lost, but the stretegic results were more than he could have hoped for. Union forces several times larger than his small army were diverted from the Union assault on Richmond to deal with the threat of Jackson. (Note: “up the Valley” in the Shenandoah means south, as the Valley gets higher in elevation the farter south you go.)

May 25 First Battle of Winchester

Thomas Jackson (16,000) vs. Nathaniel Banks (6,500)
In a surprise move, Jackson returned north via the Luray Valley, overrunning Front Royal and almost getting behind Banks’ army at Strasburg. Banks was forced to hastily withdraw from his postion at Strasburg, forming a defensive line south of Winchester. Jackson attacked early in the morning of the 25th. He outnumbered Banks by more than 2 to 1, and after three hours fighting Banks’ army fled north for the Potomac. But Jackson’s unruly cavalry were not at hand, and an ideal oportunity to destroy Banks’ army slipped through a frustrated Jackson’s fingers.

May 30 After briefly advancing as far as the Potomac, Union reinforcements closed in. Jackson withdrew back up the Valley, barely escaping being trapped between Shields’ and Fremont’s pursuing armies.
June 4 Winchester was reoccupied by the Federals
September 2 Antietam Campaign.

As Jackson descended on Harpers Ferry from the northwest Union forces under Julius White evacuated Winchester. (They would surrender a few days later at Harpers Ferry.) Confederate troops returned to Winchester, which become the supply point for Lee’s Army at the Battle of Sharpsburg (Antietam)

Late September Winchester became a major hospital for the wounded from the Battle of Sharpsburg (Antietam). After Lee’s army returned to Virginia following its defeat at Sharpsburg (Antietam) Jackson’s Second Corps went into camp around the town.
November 22 Jackson left Winchester to join Lee on the Rappahannock, leaving behind a token cavalry force under “Grumble” Jones. Jackson would never return to Winchester.
December 3 Union forces under John Geary briefly occupied Winchester. He withdrew after only a few hours due to a smallpox epidemic.
December 4 Jones’ cavalry reoccupied Winchester
December 13 Jones moved south to Strasburg, leaving Winchester unoccupied.
December 24 Union forces reoccupied Winchester.
1863
January 1 Robert Milroy’s Union division moved into Winchester. Milroy, a fervent abolitionist, took command of the Lower Valley and oppressed the pro-Confederate population.
June 13 – 14 Second Battle of Winchester

Richard Ewell (12,500) vs. Robert Milroy (7,000)

As part of Lee’s Gettysburg Campaign, the Second Corps, under Richard Ewell since the death of Jackson, were ordered to clear Union forces out of the Shenandoah Valley and move into Pennsylvania in advance of the main army. When Ewell arrived Milroy decided to fight it out, unaware of the size of Ewell’s force. Ewell flanked and took several important Union positions on the 14th. Milroy decided to retreat after dark on the 14th. But Ewell had sent part of another division to lie in wait on Milroy’s line of retreat. In a surprise night attack at Stephenson’s Depot Milroy’s army was almost completely destroyed. Ewell – and Lee – would have a clear path through the Shenandoah and all the way to Pennsylvania.

June 15 Milroy ran into a blocking Confederate force a short distance outside of town at Stephenson’s Depot just before dawn on the 15th. His army was annihilated and mostly captured in a night battle. Confederates once again returned to Winchester.
July 22-24 After his defeat at Gettysburg, Lee retreated up the Shenandoah Valley, leaving Winchester to be reoccupied by the Federals.
1864
July 1 Jubal Early’s Confederates swept through Winchester on their way to Washington D.C.
July 20 Battle of Rutherford Farm

Stephen Ramseur (3,300) vs. William Averell (2,350)
Union General William Averell’s Division was pushing south toward Winchester, guarded by the Confederate division of General Stephen Ramseur. Ramseur mistakenly believed he outnumbered the Northerners and attacked late in the afternoon. Averell counterattacked, sending Ramseur’s men flying and capturing 300 prisoners and four guns.

July 24 Second Battle of Kernstown

Jubal Early (14,000) vs. George Crook (10,000)
Union General George Crook pursued Confederate General Jublal Early’s Army of the Valley back up the Shenandoah after its raid on Washington. Crook had recoccupied Winchester and his advanced positions were on the old Kernstown battlefield when Early turned on him and sent his corps flying back across the Potomac. Early succeeded in his mission of diverting Union forces from the attack on Richmond – Grant sent back two Union corps he had just withdrawn from the Valley. But it was at the price of facing those men under Phil Sheridan, who was given orders to destroy Early once and for all.

September 19 Battle of Opequon, or Third Battle of Winchester

Jubal Early (12,000) vs Philip Sheridan (40,000).

The final battle around Winchester was the largest and bloodiest in the Shenandoah Valley. Union General Philip Sheridan attacked with 50,000 men, hoping to hit Confederate General Jublal Early’s much smaller force of 15,000 while they were dispersed on raids against Union positions. Sheridan’s force was delayed, however, and Early was able to concentrate his army northeast of town. The battle cost Sheridan 5,000 casualties and Early 3,600, including an unusual number of general officers on both sides. While Early came out ahead in the numbers of casualties they represented a much larger percentage of his army, which fled south up the Valley to Fisher’s Hill. Confederate forces had given up Winchester for the last time.

October 19 Battle of Cedar Creek

Jubal Early (21,000) vs Philip Sheridan (32,000).

A dawn surprise attack by Early on Sheridan’s camps outside Middleville, 12 miles south of Winchster, nearly routed the Union forces. Sheridan had spent the night in Winchester after returning from a meeting in Washington, and rode to rally his men and totally defeat Early. The last chance for the Confederacy to regain Winchester and retain the Valley passed.

1865
Despite guerrilla activity by Confederate partisans, Winchester remained the headquarters and supply center for Union occupation forces in the Shenandoah Valley.