To ensure academic independence, the University was established under its own Charter approved by the UN General Assembly, which authorized the University to grant degrees at the MA and doctoral levels. Although UPEACE is not subject to UN regulations and does not receive regular UN funding, it has strong links with the UN Secretary General's office and many other parts of the UN system.

UPEACE is governed by an independent Council of renowned personalities with expertise in peace and security matters. The academic quality of the programmes offered by UPEACE is ensured by an International Academic Council of eminent scholars. The Rector and a multicultural academic and management staff oversee the day-to-day operations of the entire UPEACE system.

Funding for UPEACE comes from the support of a number of donor governments, foundations, institutions and individuals who believe in the mission of the University and the quality of its programmes. Fundraising for an endowment fund is in progress.