Dr. Cowles was born in Ryegate, Vermont, and received his A.B. (1859) from Dartmouth College and his M.D. (1863) from the College of Physicians and Surgeons at Columbia University (NY). He interned at the Hartford Retreat for the Insane and then entered the Medical Corps of the U.S. Army, resigning in 1872. He settled in South Boston, was appointed Visiting Physician to Carney Hospital, and shortly after was elected Medical Superintendent of the Boston City Hospital—one of the first to have a medical rather than a lay superintendent.
In 1879, he was called to be Superintendent of the McLean Asylum in Somerville, MA, and he developed the scientific side of the hospital with proper laboratories and staff, advanced the professional training of nurses, and instituted case conferences for staff. He retired from McLean in 1903.
Dr. Cowles was Professor of Mental Diseases at Dartmouth (1866–1914), which also conferred an L.L.D. upon him in 1890. He was an instructor in mental diseases at Harvard (1888–1914), a lecturer at Clark University in Worcester, a fellow and member of numerous medical organizations, including the American Neurological Society, the American Medical Association, the Association for the Advancement of Science, and a member of Phi Beta Kappa. Dr. Cowles was President of the American Medico-Psychological Association (1894–1895).