The SEASREP Foundation is registered as a non-profit non-stock non-government organization in the Philippine Securities and Exchange Commission.

The Board of Trustees sets the policy and general direction of the organization. The Board is composed of five resident Southeast Asian scholars from various Southeast Asia universities and research institutions, two experts from anywhere in the world, and representatives of donor institutions that support SEASREP operations and programs.

The Executive Director, with the support of the program and administrative staff in Manila, oversees and manages the day-to-day operations of the organization.