The SEF Alliance is governed by a constitution and a Steering Committee comprised of one voting representative from each member organisation, as well as one voting representative from UNEP.  Non-voting representatives come from the Secretariat.  The Steering Committee meets quarterly by conference call and once in-person per year in conjunction with the annual SEF Alliance general meeting.

The Secretariat is managed by BASE (Basel Agency for Sustainable Energy) - a UNEP Collabrating Centre located in Basel, Switzerland - in collaboration with the Clean Energy Group (CEG) in the U.S., which also manages the Clean Energy States Alliance (CESA).  The Secretariat coordinates and oversees all SEF Alliance activities, including annual conferences, Steering Committee meetings, and monthly call seminars.  Staff are also responsible for administering information sharing, joint projects, and client services; managing and maintaining the website and listservs; performing specialised research; collecting and disseminating relevant, up-to-date information about initiatives and trends in the sustainable energy finance arena; developing specialised tools for use by members; and managing consultants.

The budget for the Alliance consists of two components:

1. Operational budget: This covers costs for staff time for administrative, consulting, information services, and communications; related travel; operational expenses related to meetings, call seminars, and other activities; and indirect overhead. A portion of this is covered by UNEP, another portion by the Oak Foundation, and the remainder is split among the member agencies and weighted according to the size of their budgets for relevant direct programme expenditures.

2. Discretionary contributions for joint projects: Organisations interested in specific projects, research or advising services can work with the secretariat to determine project-specific activity budgets that can be funded by one or several of the requesting member entities, as well as by any external support that can be leveraged for the project. 

On an ongoing basis, the Secretariat conducts external fundraising efforts targeting international institutions, foundations and other clean energy stakeholders that may be interested in supporting operations or activities. UNEP and the Oak Foundation provided support for start-up of the initiative.