Born in New York City on July 25, 1754, he graduated from King's College (Columbia University) in 1770 and entered military service through New Jersey state channels in January 1776.

On August 12 of the same year, an Infantry regiment was organized under Brevet Brigadier General Josiah Harmar, who then became the senior officer in the United States Army.

Doughty was designated major commandant of the Battalion of Artillery in September 1789, and then was dispatched by President Washington to the frontier to negotiate with the Choctaw Nation for trading post sites in 1789.

He was repelled with serious losses when attacked by Cherokee, Shawnee, and Muscogee people, while leading a detachment up the Tennessee River on a negotiating mission to the Chickasaw Nation in 1790.

In May 1800 Doughty resigned from the Army and returned to private life on his estate at Morristown, New Jersey, to engage in agriculture and pursue literary studies.