From 1886 to 1891, Eaton was president of Marietta College, and, in 1895, he was appointed president of Sheldon Jackson College in Sitka, Alaska. In 1898, he became inspector of education in Puerto Rico and played a role in the centralization of its educational system. At the same time, he was the president of Westminster College in Salt Lake City. He also served as Councillor of the American Public Health Association, Vice President of the American Association for the Advancement of Science and president of the Association of Social Science. He was a representative of the Interior Department at the centennial exposition and the organizer of the educational exhibit at New Orleans. He was president of the national congress of education and of the American Society of Religious Education.