IISER Pune has been ranked twentieth in a list of top Young Universities in the world published by the prestigious Nature Index. The Index classifies institutions younger than fifty years in this category. Of the ten Indian institutes which have made it to the top 100 Young Universities list, IISER Pune is second after Homi Bhabha National Institute, Mumbai. Four other IISERs are also featured in the list.

The rankings are based on the Fractional Count calculated for each institution for 2018. Fractional count (FC) takes into account the proportion of authors from a particular institution, given the number of affiliated institutions for each article (contribution of all authors considered equal), the maximum combined FC for any article being one. The total article count (AC) of the year and the highest subject-wise rank of each institute is also given in the list, along with the overall global rank (see a glossary of terms here).