At a meeting between education NGOs and the Ministry of Education, Youth and Sports (MoEYS) in August 2000, NGOs were invited to discuss and draft advice on a strategy for improving Ministry - NGO partnership in education sector management.

Following consultation and a study on a Strategic Partnership, the Education Sub-sector Working Group formally proposed the formation of an "NGO Education Partnership" under the leadership of an Interim Board.

The NEP was formally constituted a year later with the adoption of a Charter, election of a five-person Board, and signing up of seventeen member organizations.