John Henry Eaton was born on December 5, 1829, in Sutton, Merrimack County, New Hampshire.

He was an educator and Civil War veteran. He graduated from Dartmouth College, N. H. in 1854. Then he studied at Andover Theological Seminary and was ordained in 1862 to the Presbyterian ministry. He received his M.A. and L. LD degrees from Rutgers University, New Jersey. Eaton taught school in Cleveland and in Toledo (1856-1859). In 1861, he entered the American Civil War as a chaplain of the 27th Ohio Volunteer Infantry. In 1862, he was appointed superintendent of freedmen and in 1863, Major General Ulysses S. Grant appointed him the Superintendent of Negro Affairs for the Department of Tennessee, where Eaton supervised the establishment of 74 schools. In 1866, he was nominated by President Andrew Johnson and confirmed by the US Senate for the appointment of a brevet brigadier general of volunteers. General Eaton left the military and eventually returned to his career in education and became editor of the Memphis Daily Post. He was then appointed US Commissioner of Education in 1870 and served in the Bureau of Education, Washington, D.C. 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. He was also the president of Westminster College in Salt Lake City and 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 wrote a history of Thetford Academy, "Mormons of Today", "The Freedmen in the War", "Schools of Tennessee" and several reports, addresses, and magazine articles.

In 1864, he married Alice Eugenia Shirley (1844–1927). He died on February 8, 1906, in Washington, D.C. and is buried at the Arlington National Cemetery.