He joined the 1st Regiment Massachusetts Volunteer Infantry of the Union Army as a private on September 22, 1862 in Boston during the Civil War.
In New York, Emerson was associated with Willard Parker, a 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.
One of his efforts was the translation into English of David Malo's work on Hawaiian lore and customs.
Emerson has been criticized by Hawaiian royalists and historians for being a founding member of the Hawaiian League of 1887, which authored the Bayonet Constitution forced on King Kalākaua, under threat of death.