CIVICUS is governed by the Board of Directors, each of whom is elected from the CIVICUS membership or co-opted by the Board. The CIVICUS Board currently meets twice a year to provide strategic guidance to the management. Most recently, the Board was responsible for leading the process of and adopting the 2008-12 Strategic Directions.

The CIVICUS Board delegates specific policy areas of the governance work to the Board Committees. Currently, the Executive, Governance, Programme and Finance & Audit Committees are actively fulfilling respective roles. The Board is also responsible for appointing, overseeing and appraising the Secretary General.

At the staff level, the Secretary General is responsible for the day-to-day operations. CIVICUS has a management team in place, which is composed of departmental managers and coordinates on various inter-departmental issues. Currently, the CIVICUS senior management team, which provides the overall leadership for the management, is composed of the Secretary General, Deputy Secretary General-Programmes and Assistant Secretary General-Operations.