Hooker had proposed to march on Richmond after the battle at Brandy Station, but Lincoln had replied that "Lee's army, not Richmond, is your true objective." Meanwhile, Ewell's Corps was passing Front Royal and approaching Winchester.
The Union garrison was commanded by Major General Robert H. Milroy and consisted of 6,900 troops posted in Winchester itself and a detachment of 1,800 men east in Berryville, Virginia. The Union defenses consisted of three forts on high ground just outside the town. Milroy's tenure at Winchester had been marked by incivility toward the civilian population, who resented his oppressive rule, and the Confederate troops were eager to destroy his force. General-in-chief Henry Halleck did not want any Union force stationed in Winchester beyond what was necessary as an outpost to monitor Confederate movement and repeatedly ordered Milroy's superior, Maj. Gen. Robert C. Schenck of the Middle Department, to withdraw the surplus force to Harpers Ferry. Schenck, however, did not comply and, unaware that Lee's infantry were approaching, did not issue any orders for Milroy to withdraw immediately from Winchester before June 13.