IISER Pune has been ranked 23 in the overall category of the 2019 National Institutional Ranking Framework (NIRF) India Rankings. Initiated by the Ministry of Human Resource Development in 2015, this is the fourth year of NIRF's India Rankings.

NIRF uses 5 parameters to rank institutions across India. These include Teaching, Learning and Resources; Research and Professional Practices; Graduation Outcomes; Outreach and Inclusivity; and Perception. These parameters score for aspects such as faculty-student ratio, publications, citations, patents, consultancies, gender balance, and perception about the institution among peers and several other criteria for institutions across India.