The initial engagements of the Civil War on July 18, 1861, in what would become the First Battle of Bull Run, fought on July 21, took place on McLean's farm. Union Army artillery fired at McLean's house, headquarters for Confederate Brigadier General P.G.T. Beauregard, and a cannonball dropped through the kitchen fireplace. Beauregard wrote after the battle, "A comical effect of this artillery fight was the destruction of the dinner of myself and staff by a Federal shell that fell into the fire-place of my headquarters at the McLean House.”
McLean was a retired major in the Virginia militia, but was too old to return to active duty at the outbreak of the Civil War; he made his living during the war as a sugar broker supplying the Confederate States Army. He decided to move because his commercial activities were centered mostly in southern Virginia and the Union army presence in his area of northern Virginia made his work difficult. He undoubtedly was also motivated by a desire to protect his family from a repetition of his battle experience. In the spring of 1863 he and his family moved about 120 miles south to Appomattox County, Virginia, near Appomattox Court House.
On April 9, 1865, the war came back to Wilmer McLean when Confederate General Robert E. Lee surrendered to Lieutenant General Ulysses S. Grant in the parlor of McLean's house near Appomattox Court House, effectively ending the Civil War. Later, McLean is supposed to have said "The war began in my front yard and ended in my front parlor".