The NCTTCA institutional structure is made up of a Council of Ministers comprising Ministers responsible for transportation matters in each of the contracting States as the topmost policy organ. Next to the Council of Ministers is the Executive Committee, being an inter-governmental committee composed of Permanent Secretaries or their equivalents also responsible for transport matters in each of the contracting States; is primarily responsible for initiating general principles and policies governing the Secretariat.

Specialized committees which are in place to synthesize and make appropriate recommendations to the Executive Committee include:

a) Transport Policy and Planning Committee,

b) Customs and Transit Facilitation Committee,

c) Infrastructure Development and Management Committee,

d) Private Sector Investment Promotion Committee; and

e) Northern Corridor Public-Private Stakeholders Forum.

The executing organ is the Permanent Secretariat based in Mombasa, Kenya. It is charged with the responsibility of implementing the Northern Corridor Transit and Transport Agreement; and any other decisions and resolutions made by the Council of Ministers and the Executive Committee. Below is the NCTTCA Institutional Structure.

Institutional Structure of the NCTTCA