NAES was founded in 1965. Its roots are in a headmaster and headmistresses group dating back to the 1930s and in the unincorporated Episcopal Schools Association of the 1950s. A schools officer in The Episcopal Church's then department of Christian education supported the the latter group.
When the 1964 General Convention of The Episcopal Church discontinued the schools officer postion, a group of Episcopal school leaders organized and incorporated NAES. Two of these leaders were Ruth Jeknins and the Rev. John D. Verdery, for whom NAES’ two highest Awards are named.