The secretariat is the national coordinating organ of NEPHAK. It is charged with the day to day running of the organisation which includes:
- Identifying and executing the networks programmes
- Seeking donor support and accounting for any funds received
- Appointment and termination of staff and experts
The secretariat is headed by a National Coordinator appointed by the National Committee of Representatives. It is headquartered in Nairobi currently housed on Kabarnet Road off Ngong Road. The secretariat may include other staff charged with managing various programmes and departments. The current secretariat is composed of the following
| Edward Marienga |
Executive Director |
| Cephas Kojwang |
Senior Programs Officer |
| Peter Abwao |
Communications and Media Liaison Officer) |
| Petronila Khamusali |
Admin Secretary |
| Delphine Masongo |
APHIA 2 Coast |
| Antony Shiaba |
Driver |
| Catherine Modani |
Secretary |
| Lucy Ghati |
APHIA 2 South Rift) |
| Peter Kanyowareh |
Finance / Admin Manager |
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