NIBU will have five Faculties including the Library.

 The Library that will house all types of material textual and , visual from India, China, Sri Lanka, Thailand, Vietnam, Cambodia Laos, Nepal, Indonesia, Malaysia, Singapore and Japan will enjoy the status of a Faculty with an eminent Librarian holding the title of a Faculty dean.

• Faculty of Buddhism and Philosophy
• Faculty of Holistic Medicine
• Faculty of Social Sciences
• Library

Each faculty will initially comprise of the following department.
1. Faculties.
2. Departments.
3. Library.
4. Center for buddhist ayurvedic counseling and psychiatry.

1. Faculty of Early Buddhist Sources
I. Department of Pali and Sanskrit Sources
II. Department of Chinese and Tibetan Sources

2. Faculty of Early Buddhist Sources
I. Department of Pali Buddhism and Theravada
II. Department of Mahayana Buddhism
III. Department of Tibetan and Vajirayana Buddhisam

3. Faculty of Practical and Applied Buddhism
I. Department of comparative Religion
II. Department of Buddhism Mission
III. Department of Buddhism Sociology
IV. Department of Communication and Management
V. Department of Buddhist History
VI. Department of Art and Architecture

4. Faculty of Systems of Medicine
I. Department of Buddhist Ayurvedic Philosophy
II. Department of Buddhist Ayurvedic Psychology
III. Department of Buddhist Ayurvedic Psychiatry and Counseling
IV. Department of Buddhist Ayurvedic Pharmacology
V. Department of International Buddhist Systems of Medicine

5. Faculty of Social Sciences
I. Department of history
II. Department of Political Geography
III. Department of Development Economics
IV. Department of Environmental Studies
V. Department of Cooperative enterprises

6. Language, Computer and IT Unit