On the eve of the Battle of Antietam, the members of the Dunker congregation, as well as their neighbors in the surrounding community, received a portent of things to come. That Sunday, September 14, 1862, the sound of cannons booming at the Battle of South Mountain seven miles to the east was plainly heard as the Dunkers attended church. By September 16, Confederate infantry and artillery was being positioned around the church in anticipation of the battle that was fought the next day.
During the Battle of Antietam, the church was the focal point of a number of Union attacks against the Confederate left flank during the morning phase of the fighting. Most after-action reports by commanders of both sides, including Union Maj. Gen. Joseph Hooker and Confederate Maj. Gen. Stonewall Jackson, make references to the church.
At the end of the battle, the Confederates used the church as a temporary medical aid station. A sketch by well known Civil War artist Alfred Waud depicts a truce between the opposing sides held in front of the church on September 18 to exchange wounded and bury the dead. At least one account states that after the battle, the Union army used the Dunker Church as an embalming station. One tradition persists that Lincoln may have visited the site during his visit to the Army of the Potomac in October 1862.
As for the old church, it was heavily battle scarred with hundreds of marks from bullets in its white washed walls. Artillery had seriously damaged the roof and walls. By 1864 the church was repaired, rededicated and regular services were held there until the turn of the century.
After the war, the congregation built a new church in the town of Sharpsburg. Souvenir hunters took bricks from the walls of the old church which, combined with and a lack of adequate maintenance, weakened the structure. In 1921 a violent storm swept through the area, flattening the church. The land and church ruins were put up for sale and purchased by Sharpsburg resident Elmer G. Boyer. He salvaged most of the undamaged material of the building and sold the property. The new property owner built a home on the foundation of the old church and in the 1930s operated a gas station and souvenir shop on the site. This structure was removed in 1951 when the property was purchased by the Washington County Historical Society. They donated the site, then just a foundation, to the National Park Service. The church was rebuilt for the 100th anniversary of the battle in 1962 on the original foundation with as much original materials as possible and now stands as a beacon of peace on the battlefield.