From 1779-1781 he served as treasurer of the American Philosophical Society, which he was elected to in 1768.

He was a member of the board of aldermen in 1789, then served as mayor of Philadelphia 1792–1796.

Clarkson was involved in numerous businesses, notably a dry-goods store on Second Street.

[3] In 1765 he became involved inland settlement in the British colony of Nova Scotia, where a 100,000-acre township called Monckton was granted by the government in Halifax to Clarkson and several land partners including Anthony Wayne, John Hughes and Benjamin Franklin.

[4] He died in 1800 in Philadelphia, where he was interred in Christ Church Burial Ground.