IISER Pune offers integrated masters programmes (BS-MS), an integrated doctoral programme (Int. PhD) and a doctoral programme (PhD).
Admission to the master's degree is through the IISER joint admission process which provides three channels for admission: Kishore Vaigyanik Protsahan Yojana, Joint Entrance Examination – Advanced and state and central boards candidates, which require an additional IISER Aptitude Test.[4] Admission to the various PhD programmes is either with a master's degree in science or with a bachelor's degree, for the integrated PhD programme. Candidates are screened by interviews.[5] In addition to that candidates should have qualified a national level entrance exam for PhD program in science (like GATE)
The faculty is organised by various disciplines such as Biology, Earth and Climate Sciences, Physics, Mathematics, Chemistry, Humanities and Social Sciences. Interdisciplinary research is encouraged across disciplines.[6] The first batch of students graduated in 2012