General Eaton left the military and eventually returned to his career in education. He remained with the freedman bureau until he was discharged on December 18, 1865 and then became editor of the "Memphis Daily Post" in 1866. From 1867-1869 he was the state superintendent of schools of Tennessee. He was then appointed United States Commissioner of Education in 1870 and served with efficiency in the Bureau of Education where he, among other things, organized Washington, D.C.'s Board of Education and reorganized the Bureau of Refugees, Freedmen, and Abandoned Lands.