In 1861, after Virginia seceded from the Union and as the American Civil War broke out, Jackson became a drill master for some of the many new recruits in the Confederate Army. On April 27, 1861, Virginia Governor John Letcher ordered Colonel Jackson to take command at Harpers Ferry, where he would assemble and command the unit which later gained fame as the "Stonewall Brigade", consisting of the 2nd, 4th, 5th, 27th, and 33rd Virginia Infantry regiments. All of these units were from the Shenandoah Valley region of Virginia, where Jackson located his headquarters throughout the first two years of the war. Jackson became known for his relentless drilling of his troops; he believed discipline was vital to success on the battlefield. Following raids on the B&O Railroad on May 24, he was promoted to brigadier general on June 17.
Jackson rose to prominence and earned his most famous nickname at the First Battle of Bull Run (First Manassas) on July 21, 1861. As the Confederate lines began to crumble under heavy Union assault, Jackson's brigade provided crucial reinforcements on Henry House Hill, demonstrating the discipline he instilled in his men. Although under heavy fire for several continuous hours, Jackson received a wound, breaking the middle finger of his left hand; about midway between the hand and knuckle, the ball passing on the side next the index finger. The troops of South Carolina, commanded by Gen. Barnard Elliott Bee Jr. had been overwhelmed, and he rode up to Jackson in despair, exclaiming, "They are beating us back!" "Then," said Jackson, "we will give them the bayonet!" As he rode back to his command, Bee exhorted his own troops to re-form by shouting, "There is Jackson standing like a stone wall. Let us determine to die here, and we will conquer. Rally behind the Virginians!" There is some controversy over Bee's statement and intent, which could not be clarified because he was killed almost immediately after speaking and none of his subordinate officers wrote reports of the battle. Major Burnett Rhett, chief of staff to General Joseph E. Johnston, claimed that Bee was angry at Jackson's failure to come immediately to the relief of Bee's and Francis S. Bartow's brigades while they were under heavy pressure. Those who subscribe to this opinion believe that Bee's statement was meant to be pejorative: "Look at Jackson standing there like a stone wall!"