Jonathan Clark received a fair English education, and was a lawyer and successful business man.

His first public office was as deputy clerk of Spottsylvania county, Virginia. In 1772 he removed to Woodstock and was a delegate from Dunmore county with Peter Muhlenberg in 1775 to a convention at Richmond to consider the interests of the colonies.

He opposed Governor Dunmore, and in 1776, with a company of volunteers, of which he was Captain, forced him to take refuge on an English ship. In June, 1776, he marched with Muhlenberg's regiment to Charleston, South Carolina, and was with Washington's army at Bound Brook, New Jersey, in 1777, participating in the battles of Brandywine and Germantown. He was in the battle of Monmouth, 1778, and in 1779 at Paulus Hook, where he was second in command, having been promoted major by congress; and his conduct on this occasion won for him the commission of lieutenant colonel from congress.

He marched with his Virginia regiment to Charleston, South Carolina, in 1780, and surrendered with General Lincoln on May 12, 1780. He was held a prisoner in Charleston until the spring of 1781, when he was paroled.

He and his wife, Sarah, settled in Spottsylvania county, Virginia, and in 1793 Colonel Clark was commissioned a major general of Virginia militia. In 1802 he joined his brother, George Rogers, at the falls of the Ohio, settling at Trough Spring, near Louisville, Kentucky, where he accumulated a large property which he left to his widow and six surviving children. He died suddenly at his home.