In 1756 he joined the Lancaster company and was commissioned as an ensign. He served on the Forbes Expedition to Fort Duquesne in 1758, and by 1759 he was a Captain. In 1776 Pennsylvania began raising new units for the Continental Army, and on March 21, 1776, Atlee was named Colonel of a unit, the Pennsylvania Musketry Battalion. Once they were organized, he led them north to the defense of New York City. During the Battle of Long Island on August 27, 1776, he led the original defense of the Old Stone House in Brooklyn, New York. The house was situated on high ground and covered the American withdrawal. Atlee's force was driven from the house, but General William Alexander came to support him. The Americans twice recaptured the house. The defenders directly engaged three British regiments, led by General Cornwallis. They held out until noon, allowing most of the Continental forces in Brooklyn to successfully withdraw to the Brooklyn Heights. At last, surrounded and cut off by the Hessians, General Alexander surrendered in the early afternoon. While watching this action from fortifications to the north on Brooklyn Heights, General Washington remarked, "Good God, what brave men must I lose this day!" Samuel Atlee remained a prisoner of war until he was exchanged in October 1778.
Political career
When Atlee returned home, the Pennsylvania Assembly named him as a delegate to the Continental Congress. He served there until 1782. In 1782, Lancaster County sent Atlee to the Pennsylvania Assembly. In 1783, he became a charter member in the Pennsylvania branch of the Society of the Cincinnati, and was named the County executive for Lancaster County. In 1784 he served on the commission negotiating Indian treaties that acquired most of the remaining Native American lands in Pennsylvania. Atlee was returned to the state assembly in 1785 and 1786. He died on November 25, 1786 while attending a meeting of the legislature in Philadelphia, and is buried in the Christ Church Burial Ground there. The reconstructed Old Stone House that he defended in the battle of Brooklyn located at the corner of Fourth Avenue and Third Street, it was moved a few feet during its reconstruction and is at a higher grade level. It is in Byrne Park, and is open to the public on a limited basis.