He was the son of Patrick Doherty (1794–1849) who came from Ireland to New York City about 1811, and fought in the War of 1812.
John Doherty studied law, was admitted to the bar in 1847, and commenced practice in New York City.
After the death of his father, he abandoned the law and looked after his father's business instead.
He was a member of the New York State Senate (7th D.) in 1858 and 1859.
He died on the day after the Legislature adjourned in April 1859.