Upon graduation, Skinner took a job at his alma mater as an assistant chemist, and enrolled in graduate school at Columbian University (now the George Washington University) in 1896. He graduated with an M.S. from Columbian in 1898. In 1899, Skinner married Georgia née Mitchell, with whom he later had a daughter. From 1899 to 1901, he served in an assistant chemist post at the University of Arizona. While there, he also studied geology and coached the football team in 1900 and 1901. He guided Arizona to 3–1 and 4–1 records, respectively.