The Commission is headed by the Director-General and has seven (7) departments namely:
i. Internal Boundaries
ii. International Boundaries
iii. Maritime Boundaries
iv. Research and Policy Analysis
v. Admin and Supplies
vi. Legal Services
vii. Finance and Accounts
The National Boundary Commission has Zonal Liaison offices to further strengthen the activities of the Commission by means of coordinated activities to enhance amicable resolution of disputed boundaries.
Presently, the Commission has Six (6) Zonal Liaison Offices in each of the geopolitical Zone in Lagos (South West), Calabar (South-South), Enugu (South East), Sokoto (North West), Minna (North Central) and Maiduguri (North East).