In 1831, Baugher became a teacher of classical studies at the Gettysburg Gymnasium, which was then under the Seminary. The Gymnasium became Pennsylvania College (now Gettysburg College) in 1832. Baugher was selected as professor of Greek and the Belles Lettres. He served in this position for 18 years, and also served as the Secretary for the Faculty of the College. He was ordained a Lutheran pastor in 1833. His brother, Isaac, became a College trustee in 1844 and gave the College its first bequest.