Warren graduated from Harvard College in 1759 and obtained his Master of Arts degree in 1762. His thesis was, "Do all diseases arise from obstruction?" which he answered in the negative. He studied medicine under Dr. James Lloyd, a staunch Loyalist. Warren began his medical practice in 1763 at the age of 22, and his extensive patient list included patriots such as John Adams and John Hancock, as well as the most prominent British officials who would remain loyal to the Crown: the Hutchinson, Oliver, Hallowell, and Flucker families.
By the late spring of 1763, having completed his medical apprenticeship with Dr. Lloyd, Warren opened his own practice in Boston. The services he provided ranged from treating "venereal disease" to "reducing fractures and dislocations." He also ran a full-service apothecary shop. Unlike many Boston physicians, he provided obstetrical care to pregnant women, as did his mentor, Dr. Lloyd and many female midwives.