Ph.D. programs at IIST are offered in a range of disciplines, including Aerospace Engineering, Avionics, Earth System Science, Mathematics, Physics, Chemistry, and Humanities and Social Sciences. Students can enroll under two categories: externally funded (e.g., CSIR, UGC) or institute-funded.

Upon admission, students complete coursework to earn the required credits. By the end of the second year, they must pass a Comprehensive Examination, which upgrades their status from Junior Research Fellow (JRF) to Senior Research Fellow (SRF). Following this, they continue their research under the guidance of a supervisor in their chosen area of interest.

The institute supports research dissemination by offering travel grants to attend national and international conferences. Institute fellowships are available for up to five years, with emoluments aligned with those provided by other government agencies such as CSIR and UGC.