IISER Pune began functioning in the NCL campus in 2006. During 2007-2008, it moved to a hired transit campus, where the essential components such as classrooms, teaching and research laboratories (chemistry, biology and physics), and library were immediately established.

In the year 2012, IISER Pune, along with four other IISERs, was declared as an Institute of National Importance through an Act of Parliament.

IISER Pune is now located on a 98-acre land, generously made available by CSIR-NCL. The campus has 37,000 sq. mt of academic space and 80,000 sq. mt of residential space. It is modern, with green, energy efficient and environmental friendly buildings, conforming to GRIHA 4 star rating. In addition to a modern lecture hall complex, research laboratories and main academic building, the campus houses a 128-room guesthouse - cum - mini convention centre, students’ hostels, guest rooms, and a central dining place. The campus also hosts faculty and staff housing, and a  modern outdoor and indoor sports complex.