After graduation he studied medicine under Dr. Joseph Warren, a well-known Patriot political leader. When the Battles of Lexington and Concord sparked the American Revolutionary War in April 1775, Warren and Eustis both worked in the field, tending the injured revolutionaries. Warren secured for Eustis a commission as regimental surgeon to the rebel artillery. Eustis helped care for the wounded at the June 1775 Battle of Bunker Hill, in which Warren was killed. He served with the Continental Army in the New York and New Jersey campaign, refusing a lieutenant colonel's commission offered by artillery chief Henry Knox. During his Continental Army service, Eustis met and established an enduring friendship with New Jersey native Aaron Burr.