Warren joined Colonel Pickering's Regiment in 1773 as an army surgeon. On June 17, 1775, he was in Cambridge tending to the wounded coming in from the Battle of Bunker Hill on Breed's Hill over four miles away. Worried about his brother Joseph, who had joined the fighting and died, Warren went to search for him after the battle was over. A British sentry told John he could not pass and then bayoneted him as a warning, forcing the depressed Warren to go back to Cambridge.