He attended Williams College in Williamstown, Massachusetts and served in the First Regiment of the Massachusetts Volunteer Infantry during the Civil War, during which he was wounded three times. After graduating from Williams in 1865, he studied at Harvard and the Columbia University College of Physicians and Surgeons in New York City, from which he graduated in 1869. This was followed by work at Bellevue Hospital in New York City. In New York Dr. Emerson was associated with Dr. Willard Parker, the eminent surgeon, as student and assistant. For several years he was also clinical assistant to Dr. Seguin, professor of nervous diseases at the College of Physicians and Surgeons. He served as a doctor in New York until 1878, after which he relocated to Hawaii.