Born in Boston, he was the son of John Warren, well-known doctor, Harvard professor, and a founder of the Harvard Medical School and the nephew of Dr. Joseph Warren. He graduated from Harvard College in 1797, then began the study of medicine with his father. In 1799, he continued his medical studies in London and Paris and Edinburgh, including work with the pioneer anatomist Sir Astley Cooper (1768–1841). He graduated with an M.D. from the University of Edinburgh Medical School in 1801. On his return to America in 1802, Warren entered into partnership with his father and also assisted him with anatomical lectures, dissections, and demonstrations at Harvard Medical School. By 1806, Warren had begun performing cataract extractions for a condition which was most likely angle-closure glaucoma.