| Department | Academic Programmes | ||
| Department of Animal Sciences | MSc | MPhil | PhD |
| Department of Biochemistry | MSc | MPhil | PhD |
| Department of Biotechnology | - | MPhil | PhD |
| National Centre for Bioinformatics | - | MPhil | PhD |
| Department of Environmental Sciences | MSc | MPhil | PhD |
| Department of Microbiology | MSc | MPhil | PhD |
| Department of Plant Sciences | MSc | MPhil | PhD |
| Computer Centre | PGD IT, PCIT, PCBIT | ||
| Department of Chemistry | MSc | MPhil | PhD |
| Department of Computer Sciences | MSc | MS | PhD |
| Department of Earth Sciences | MSc | MPhil | PhD |
| Department of Electronics | MSc | MPhil | PhD |
| Department of Mathematics | MSc | MPhil | PhD |
| Department of Physics | MSc | MPhil | PhD |
| Department of Statistics | MSc | MPhil | PhD |
| Institute of Information Technology | MIT | ||
| Area Study Centre (ASC) | - | MPhil | PhD |
| Department of Anthropology | MSc | MPhil | PhD |
| Department of Defense & Strategic Studies | MSc | MPhil | PhD |
| Department of History | MSc | MPhil | PhD |
| Department of Sociology | MSc | - | - |
| Centre of Excellence in Gender Studies | MSc | - | - |
| National Institute of Pakistan Studies(NIPS) | MSc | MPhil | PhD |
| National Institute of Psychology (NIP) | MSc | MPhil | PhD |
| Quaid-i-Azam School of Management Sciences (QASMS) | MBA/MPA | MPhil | PhD |
| School of Economics | MSc/MPA | MPhil | PhD |
| School of Politics and International Relations | MSc | MPhil | PhD |
| Taxila Institute of Asian Civilizations (TIAC) | MSc | MPhil | PhD |