The GFCM is governed by the decisions of its 23 contracting parties. It holds statutory sessions on an annual basis to review the implementation of its yearly workplan, adopt recommendations and resolutions, endorse its autonomous budget, and agree on its future priorities and direction. It can convene special or extraordinary sessions at the request or with the approval of the majority of its members.

The sessions of the Commission are attended by member delegates, experts, advisers and observers. Each member has the right to one vote, except in the case of a regional economic integration organization, such as the European Union, which is entitled to the number of votes equal to the number of its member states that are also members of the GFCM. Regional economic integration organizations cannot exercise their votes when their member states exercise theirs and vice versa.

The GFCM also sees the participation of select cooperating non-contracting parties, and allows relevant partner organizations to contribute as observers.

As regulated in the GFCM Agreement, the Commission is coordinated by a Bureau.