The idea of a National Agriculture Education College originates from an agreement signed between the governments of Afghanistan and the Netherlands in 2009. At the time, it was agreed that the Dutch government would assist the Afghan government with improving the quality of vocational agricultural education in Afghanistan. One of the main results of this has been the establishment of NAEC, the first dedicated institute for training teachers of agricultural high schools. Thus, NAEC was initiated through a partnership between the Government of Afghanistan and the Government of the Netherlands, with the Dutch Government providing initial funding and Wageningen University and Research Centre contracted as lead implementing agency.

Preparations for establishing NAEC started soon after the agreement was signed, and over a two-year period, over 30 Afghan students received their Master’s training at the Van Hall Larenstein Institute of Applied Sciences (at that time part of Wageningen University and Research centre) in the Netherlands. In November 2011, half of the graduates returned to Afghanistan to become the first teachers at NAEC. Lessons started in April 2012. Together with Wageningen University and Research Centre the entire curriculum for NAEC was created from the ground up.

Even though NAEC is set up in collaboration between the Netherlands and Afghanistan, all staff at NAEC is Afghan. The college only works with international consultants for short-term periods.

The organisation is set up as a semi-autonomous institute, with a supervisory board that includes representatives from the Deputy Ministry of Technical and Vocational Education and Training, (DMTVET) and the private sector. Currently, NAEC generates income through the provision of consultancy services, while continuing to receive welcome contributions from donor agencies. The Government of Afghanistan has provided the land on which the campus and farm are established.