Day to day political coordination of the Coalition rests in the hands of the Coalition Chair. The chair of the Coalition rotates among member states on an annual basis. The chair provides diplomatic support and coordinates the overall FOC activities and meetings alongside the international conferences. Past chairs have also hosted the annual FO Conferences in The Hague, Nairobi, Tunis Tallinn, Ulaanbaatar and San Jose. The current chair of the Freedom Online Coalition is Costa Rica.

The Chair is assisted by the Friends of the Chair, a group of FOC members currently comprising Argentina, Canada, Costa Rica, Estonia, Germany, Netherlands, Norway UK, USA. The group provides support to the current chair to assist with the diplomatic work and the preparation of the annual FO Conference and ensure continuity from year to year.

In 2013, the Coalition further established issue-specific working groups that continue dialogue in-between formal FOC meetings. Throughout the year, these multistakeholder working groups for 15-20 members form work towards practical outcomes on key issues of concern to Internet freedom and human rights.

The FOC Support Unit is a neutral, third party secretariat that provides a range of administrative and coordinative assistance to the Coalition and its members. It also acts as a point of contact for anyone wishing to know more about the work of the Coalition. Currently, this function is held by Global Partners Digital, a social purpose company based in London.