Skene was born in Fyvie, Scotland, on 17 June 1837. At the age of 19, he went to North America. He studied medicine at King's College (now the University of Toronto), then at the University of Michigan, and finally at the Long Island College Hospital (now the State University of New York Downstate Medical Center) in Brooklyn graduating in 1863. From July 1863 until June 1864, he was acting assistant surgeon in the U. S. Army, after which he entered private practice in Brooklyn and advanced to become Professor of Disease of Women at Long Island College Hospital. He was professor of gynaecology in the post-graduate Medical School of New York in 1884, and was president of the American Gynaecological Society.