John Warren was born on July 27, 1753 in Roxbury, Massachusetts, and died on April 4, 1815 in Boston. He was the son of Joseph Warren, a prosperous farmer, and Mary Warren. In 1777, he married Abigail Collins, with whom he had 17 children. He is remembered as a physician, anatomist, surgeon, and medical educator. Warren graduated with an A.B. degree in 1771 from Harvard College. He subsequently studied medicine with his brother Joseph, a Revolutionary War hero, and in 1786 received an honorary M.D. degree from Harvard University. From 1774 to 1775, he had a brief and not entirely successful medical practice at Salem, Massachusetts. From 1775 to 1777, he served as hospital surgeon during the siege of Boston and the New York-New Jersey campaign. From 1777 to 1782, he was in charge of the Continental Army hospital in Boston. Between 1780 and 1782, he delivered three series of anatomical lectures, the last two sponsored by the Boston Medical Society. From 1783 to 1815, he was a member of the (original) faculty of Harvard Medical School, where he became the first Hersey Professor of Anatomy and Surgery. From 1804 to 1815, he served as seventh president of the Massachusetts Medical Society. He was active in community affairs, serving as grand master of the Massachusetts Lodge of Free and Accepted Masons. He was a founder and president of the Massachusetts Humane Society; a founder of the Anthology Club; a trustee and manager of the Massachusetts Charitable Society; a trustee of the Massachusetts Agricultural Society; a member of the editorial board of Boston Magazine; and a fellow of the American Academy of Arts and Sciences. Although gifted as an anatomist, surgeon, and teacher, John Warren is also remembered as being ambitious to the point of harshness and self-righteous to the point of disagreeability.

Warren was the single most important person in the early institutionalization of Boston medicine. He gave public lectures on anatomy toward the end of the Revolution. As a surgeon, Warren successfully amputated at the shoulder joint (1781), performed an abdominal resection (1785); and excised the parotid gland (1804). Upon his death in 1815, John Warren was succeeded as Harvard's Professor of Surgery by his son, John Collins Warren, who would later become the first American to operate under ether anesthesia. Warren's writings include A View of the Mercurial Practice in Febrile Diseases (1813).