On August 27, 1776, the house was an important location in the Battle of Long Island. Stirling ordered all of his troops, except a contingent of Maryland troops under the command of Major Mordecai Gist, to cross the creek. This group of Maryland troops became known to history as the Maryland 400, although they numbered about 260–270 men. Stirling and Gist led the troops in a rear-guard action against the overwhelming numbers of British troops which surpassed 2,000 troops supported by two cannon. Stirling and Gist led the Marylanders in two attacks against the British, who were in fixed positions in and in front of the Vechte–Cortelyou House.

After the last assault the remaining troops retreated across the Gowanus Creek. Some of the men who tried to cross the marsh were bogged down in the mud under musket fire and others who could not swim were captured. Stirling was surrounded and, unwilling to surrender to the British, broke through the British lines to von Heister's Hessians and surrendered to them. 256 Maryland troops were killed in the assaults in front of the Old Stone House and fewer than a dozen made it back to the American lines. Washington, watching from a redoubt on nearby Cobble Hill, at the intersection of today's Court Street and Atlantic Avenue, was reported to have said, "Good God, what brave fellows I must this day lose!".

After its capture, the house was used as an artillery position by an estimated 2,000 British and hired Hessian soldiers who fired on the Americans, who had already suffered disastrous losses and were fleeing from the east to the American forts across the Gowanus Creek to the west. Some four hundred soldiers of the Maryland Brigade under Colonel William Smallwood regained the house twice that day, but were finally repulsed by the British, with very heavy casualties.