John Eaton Jr. was born on December 5, 1829, in Sutton, New Hampshire, the first of John Henry and Janet Collins (Andrews) Eaton's nine children. Eaton graduated from Dartmouth College in 1854, after which he served as the Superintendent of Schools in Toledo, Ohio. He later studied theology in Andover, Massachusetts, and was ordained a Minister of the Gospel by the Presbytery of Maumee in 1861.

When the Civil War broke out, Eaton enlisted in the 27th Ohio Infantry as a chaplain. In November 1862, General Ulysses Grant put Eaton in charge of the contraband camps, which cared for and organized the numerous formerly enslaved people who had escaped to freedom behind Union lines. Eaton's excellent service in this position earned him a commission as a Colonel of the 63rd U. S. Colored Infantry, and in 1866 he was appointed Brevet Brigadier-General. Eaton married Alice Eugenia Shirley (1844-1927) on September 29, 1864, and resigned his military commission three months later.

In May 1865, Eaton moved to Washington, D.C., to take a position as the assistant commissioner of the newly formed Freedmen's Bureau. He soon left this position in order to publish The Memphis Post (1866-1867), a pro-Union newspaper. He was elected Superintendent of Schools in Tennessee in 1867 and became the U.S. Commissioner of Education in 1870. After his resignation due to poor health in 1886, Eaton served as President of Ohio's Marietta College (1885-1891) and of Utah's Sheldon Jackson College (1895-1899). He began work on Puerto Rico's public school system during the American military occupation of 1899 but resigned in 1900 due to continuing poor health. John Eaton Jr. died in Washington, D.C., on February 9, 1906, and is buried in Arlington National Cemetery.

Eaton and his wife Alice had three children: sons James Shirley and John Quincy, and daughter Elsie Janet Eaton Newton, who later followed in her father's footsteps to become an educator with the United States Indian Service, and later Dean of Women at both Cornell and Marietta Colleges.