It had been his custom at family prayers to ask of God protection from sudden death, but for some time before his death he ceased to do so. His family noticed this, and one of them asked his reason for the omission. He answered quietly, "The Lord knows best."
On the 25th of March, 1869, he was at his usual post in his office, and after business hours, as was his habit, set out with his daughter for a drive in the Central Park, As he neared the Park the pole of his carriage broke suddenly, and the horses, becoming frightened, dashed off furiously, dragging the carriage after them. Mr. Harper and his daughter were both thrown violently upon the pavement. The latter was but slightly injured, but Mr. Harper was taken up insensible, and conveyed to St. Luke's Hospital, which was close at hand. He never regained consciousness, but lingered until fifteen minutes after seven on the evening of the 27th, when he expired, surrounded by all his family, excepting his wife, who had long been an invalid. His death was regarded as a calamity to the city, and all classes of the community united to do honor to his memory.