UTNU is governed by the General Assembly which is the supreme organ of the organization. The General Assembly meets once a year to evaluate the activities of the organization. Under the General Assembly, there is a Board of Directors. The Board is the key policy-making and governing body of the organization and works independently. It formulates and approves policies, and organizational systems to help in strategic planning and evaluate the overall performance of UTNU on a periodic basis. The Board of Directors consists of 9 members (5 female and 4 male) and is headed by its Chairperson. The organization’s board of directors comprises development professionals, intellectuals, academicians, activists, and media persons. The Executive Director of UTNU serves the board as the secretary and ex-officio member.

Project activities are overseen by the Executive Director (ED) who reports to a 9 Member Board of Directors and is responsible for the overall management of the organization. The Executive Director is supported by the programs manager and a team of coordinators or managers of different sections or programs of the organization and they jointly form a management structure for the organization.

UTNU has 15 permanent staff, 11 part-time staff, and 10 volunteers that are qualified and experienced in the fields of community development, HIV/AIDS Prevention activities, Care and treatment, Gender-Based Violence, Primary and Secondary Education, Environment Conservation, support services as well as management of Health-related information among young people and grassroots.

UTNU has built its capacity through mentoring, training, and the creation of a learning organization where staff is updated on best practices. The team is responsible for program coordination, general administration, and management, financial management supervision, implementation of program activities, monitoring and evaluation, and report preparation.