The National Park Service manages all aspects of the planning and design of the memorial, manages the operations of the temporary memorial, and will administer the Flight 93 National Memorial as a unit of the National Park System. The National Park Service is the agency under which the Advisory Commission operates.

The Flight 93 Advisory Commission is a federal commission, Congressionally chartered, and appointed by the Secretary of the Interior. It is comprised of fifteen members, including family members of the Flight 93 passengers and crew, local residents and officials, national figures, and a representative of the Director of the National Park Service. Public Law 107-226 was signed by the President on September 24, 2002, and established the Commission as the legislated body with the authority to make recommendations to the Secretary of Interior on:

1) the design of a permanent memorial to the Secretary of the Interior and to Congress by September 25, 2005; (completed)

2) the management plan for the national memorial to the Secretary; (completed; Record of Decision signed July 2007); and

3) the boundary for the national memorial to the Secretary. (completed; approved by the Secretary of Interior January 2005).

As an advisory body, the Commission hears reports and proposals from the Task Force, deliberates and sends forward recommendations to the NPS and Department of the Interior leadership, as requested. The Commission will sunset at the opening of the permanent memorial.

The Flight 93 Memorial Task Force  is an unincorporated, grassroots organization, and provides a voice for all interested and concerned parties in planning and designing the memorial. The Task Force nominated members for the Flight 93 Advisory Commission in 2003, and serves as the Commission’s operational arm. The Task Force’s approximately 80 – 90 members include family members, community members, first responders, educators, and other local, regional, and national stakeholders. This working group provides all of the information and proposals necessary for the Advisory Commission to make its recommendations to the Secretary and Congress, and is a way for the public to be involved. Committees of the Task Force include, but are not limited to the following: family memorial, archives, temporary memorial management, land acquisition, design oversight, interpretive planning, fundraising, friends group, and other ad hoc committees as needed. Representative members of each of the partner organizations sit on each committee. Committees meet either on a regular, or on an as-needed basis.

The Families of Flight 93, Inc. is a private non-profit 501(C) 3 organization established to assist in developing and sustaining a permanent memorial to the crew and passengers of United Airlines Flight 93. A fifteen-member board of directors presides over the operations, and maintains communication with the immediate and extended family members of the passengers and crew of Flight 93.

The National Park Foundation administers the Capital Campaign, with two full-time dedicated staff, plus the administrative support of the Foundation. The congressionally-chartered Foundation is the national charitable partner of America's national parks.