He served as a pastor at the Arlington Avenue Presbyterian Church in East Orange, New Jersey from 1893 to 1908. In 1908, he was appointed President of Middlebury College. While president of Middlebury, Thomas oversaw the founding of two of its most prestigious institutions, the Middlebury College Language Schools in 1915 and the Bread Loaf School of English in 1920. In addition, he guided a rapid expansion of Middlebury's main campus from four buildings to nine. McCullough Gymnasium (1912) Voter Hall (1913) Mead Chapel (1914), and Hepburn Hall (1917) formed the edges of what is now Middlebury's Main Quadrangle, and Pearson's Hall (1911) became the first building constructed for the women's college. He continued to serve as Middlebury's president until 1921, when he became President of the Pennsylvania State College (now a University). He left Penn State in 1925.
