John was born at his father's plantation of Poynton Manor in Charles County. His family had been prominent since early colonial days when William Stone had served as governor a hundred years before his birth. His parents were David and Elizabeth Stone. His elder brothers included Thomas and Michael. John had been baptized in the Anglican Church. After the split caused by the revolution he was an active Episcopalian. He married Anne Couden in February 1781, and the couple would have six children, five of whom lived to adulthood: Couden, Anne, Elizabeth, Robert Couden, and Thomas.
Revolutionary War
In 1775, Stone joined the newly organized Maryland Battalion led by Colonel William Smallwood as a Lieutenant. He was soon promoted to Captain of the battalion's first company. The battalion became part of the 1st Maryland Regiment of the Continental Army, and went north to fight in the war. They fought in the Battles of Brooklyn and White Plains. Then, in late 1776, when Smallwood was promoted to Brigadier General, Stone became the Lieutenant Colonel of the regiment. When the Continental Line was re-organized early in 1777, General Smallwood had earned additional responsibility as a brigade commander. Stone was made Colonel and commander of the 1st Maryland. He led the regiment in the Battles of Princeton, Brandywine, and Germantown. He was wounded at Germantown and as a result was lame for the rest of his life. Colonel Stone was back in active command by the Battle of Monmouth. His unit was active in the continuing defense of New Jersey. His career ended when he was wounded again in the Battle of Stony Point on July 14, 1779. This time his wounds were more serious and he resigned his commission on August 1.
Political career
Stone returned home to Maryland and was made a member of the state's Executive Council. He served there from 1779 until 1785. Charles County elected him to the Maryland House of Delegates in 1785. He was returned annually until 1787, and again in 1790. Stone was then returned to the state Council in 1791 and 1792. John was elected to a single three-year term as Governor of Maryland, and served from 1794 to 1797 before returning to private life. He died in 1804 at Annapolis, Maryland at the age of 55, and was buried there.