In late August 1862, Robert E. Lee faced a growing threat. Union General John Pope's Army of Virginia was being reinforced by troops from George McClellan's Army of the Potomac, and Lee knew he had to strike before the combined force became overwhelming. His solution was breathtakingly risky: split his army in half. He sent Stonewall Jackson with 25,000 men on a 50-mile flanking march around Pope's right, through Thoroughfare Gap, to strike the Orange and Alexandria Railroad, Pope's lifeline. On August 26, Jackson's men captured and destroyed the massive Union supply depot at Manassas Junction, then melted north to take up defensive positions behind an unfinished railroad grade on the old Bull Run battlefield. The trap was set.

Pope, convinced he had Jackson cornered, threw his forces piecemeal against the Confederate line on August 29. Wave after wave of Union troops charged into the woods west of Sudley Road, where hand-to-hand combat erupted among the trees. Maxcy Gregg's South Carolina brigade, nearly out of ammunition after eight hours of fighting, refused to retreat. Gregg lopped wildflowers with an antique Revolutionary War scimitar and told his men, "Let us die here, let us die here." Meanwhile, Pope refused to believe that Longstreet's 25,000-man wing had arrived on the field, even after multiple subordinates reported encountering Confederate troops south of the Warrenton Turnpike. His orders to Fitz John Porter to attack Jackson's flank went undelivered for two hours when the courier got lost. All day, Pope fought a battle shaped by intelligence he wished were true rather than intelligence that was.

On August 30, Pope ordered a massive assault, still believing the Confederates were retreating. Ten Union brigades numbering 10,000 men charged across open pastures into Jackson's fortified line. Temperatures exceeded 90 degrees. In what became the battle's most famous incident, Confederate soldiers ran out of ammunition and hurled large rocks at the 24th New York, who threw them back. Jackson's line nearly broke. Then Longstreet unleashed his counterattack. His 25,000 men in five divisions swept forward, overwhelming the 2,200 Union defenders south of the turnpike. The 5th New York Zouaves, wearing brilliant red and blue uniforms, suffered almost 300 casualties out of 500 men in the first ten minutes, the largest single-battle loss of any infantry regiment in the entire Civil War. One of Hood's officers wrote that the bodies on the hillside reminded him of the Texas countryside when the wildflowers bloomed.

Unlike the panicked rout that ended the First Battle of Bull Run, the Union withdrawal on the evening of August 30 was quiet and orderly. Regular Army troops under George Sykes held Henry House Hill long enough for the rest of the army to cross Bull Run and reach Centreville. Union casualties totaled about 14,000 out of 62,000 engaged. Confederate losses were roughly 8,000 out of 50,000. Pope was relieved of command on September 12 and spent the rest of the war in Minnesota dealing with the Dakota War of 1862. His subordinate Fitz John Porter was court-martialed for his actions on August 29, a verdict not reversed until 1886 when a commission found that Porter's reluctance to attack Longstreet had probably saved Pope's army from an even greater disaster.

Lee wasted no time exploiting his victory. On September 3, the vanguard of the Army of Northern Virginia crossed the Potomac River into Maryland, beginning the campaign that would culminate at the Battle of Antietam, the bloodiest single day in American history. The Second Battle of Bull Run confirmed Lee and Jackson as the most formidable command partnership of the war, while the controversy over Longstreet's performance foreshadowed the arguments that would surround him after Gettysburg. Today, the battlefield is preserved within Manassas National Battlefield Park, where the American Battlefield Trust has acquired and preserved portions of the Second Bull Run battlefield in more than 10 transactions since 2000.