During his life Warren was honored both at home and abroad for his work. He was a fellow of the American Academy of Arts and Sciences (1900), and an honorary fellow of the Royal College of Surgeons (1900). The honorary degree of LL.D. was conferred on him by Jefferson College (1895). From 1873 to 1881 he was editor of the "Boston Medical and Surgical Journal" and in 1896 served as president of the American Surgical Association. He published "Surgical Pathology and Therapeutics" (1895); "The Anatomy and Development of Rodent Ulcer"; "Pathology of Carbuncle and Columnal Adipose"; "The Healing of Arteries after Ligature in Men and Animals;" and edited the "International Textbook of Surgery" (1900).