Keenan, who was born in Bellevue, Pennsylvania, graduated in 1929 from the University of Arizona and obtained his PhD from the University of Chicago in 1932. He worked initially at Chicago's Yerkes Observatory from 1929 until 1942 when he joined the Bureau of Ordnance. With the return of peace, Keenan was appointed to the staff of the Perkins Observatory of Ohio State University, becoming professor of astronomy in 1956.

Keenan is best known for his work with William Morgan and Edith Kellman on their Atlas of Stellar Spectra with an Outline of Spectral Classification (1943). It was this work that formed the basis for the MKK system of classifying stars by their luminosity in addition to their spectral type.