The organization is under the control of the Board of Trustees (BoT) who meet periodically to formulate policies and approve programs for the organization. The BoT also assist in raising funds for projects. Among other duties, the Board also approves budget, champions the organization's cause and represent it in the larger community.

The management of NIWOSEC is headed by the Executive Director / Lead Strategist, who is the Chief Executive Officer. He is responsible for the overall administration of NIWOSEC and manages its day-to-day activities. The Executive Director is also a member of the Board of Trustees and reports to the Board.

The Executive Director provides leadership for the various departments and units of NIWOSEC.The various departments and units in NIWOSEC are as follows:

NIWOSEC appoints respectable persons who are specialists and professionals to help in providing advice and consultancy services and also enhance the brand name.

These will include: academic advisor, media advisor, governance advisor, fundraising advisor, inter-governmental advisor, amongst others.