He was born in Indiana. He studied at the University of Illinois, gaining a degree in science in 1927 and a PhD in chemistry two years later.
As a member of National Research Council he moved temporarily for academic work in Munich before he returned to the States in 1931. On return he was approved as an assistant at Rockefeller Institute, the post he held until 1948. He later became Professor of Biochemistry at University of California, Berkeley, and in 1918 Chairman of the Biochemistry Department.
Stanley's work contributed to knowledge on lepracidal compounds, diphenyl stereochemistry and the chemistry of the sterols. His researches on the virus causing the mosaic disease in tobacco plants led to the isolation of a nucleoprotein which displayed tobacco mosaic virus activity.