In addition to the University of Pune, Pune is home to several research institutions of national importance. Located adjacent to the university is the National Chemical Laboratory, one of the Indian Institutes of Science Education and Research (IISER) and the Centre for Materials for Electronics Technology (C-MET), while the university campus houses the Centre for Development of Advanced Computing (C-DAC), Inter-University Centre for Astronomy and Astrophysics, the National Centre for Radio Astrophysics and the National Centre for Cell Science.

The KEM Hospital Research Centre, Central Water and Power Research Station (CW & PRS), National Institute Of Bank Management (NIBM), NIC [National Informatics Centre], the Indian Institute of Tropical Meteorology, the Agharkar Research Institute and the Automotive Research Association of India (ARAI), and the National AIDS Research Institute are all in or around Pune.

The Bhandarkar Oriental Research Institute was established in 1917 and is a world-renowned institute for research and instruction in the Sanskrit and Prakrit languages and houses more than 20,000 ancient manuscripts. The National Institute of Virology and National Insurance Academy are located in Pune. Pune also houses the Tata Research Development and Design Centre, a research unit of Tata Consultancy Services, working in the areas of computer science and modeling/simulation for materials processing.