IISERs have a PhD program and the first few scholars have graduated from the institute during last two years. At present there are about 230 students at various levels in the PhD program in biology, chemistry, mathematics, physics, earth and environmental sciences, and, humanities and social sciences. The PhD program at IISER Mohali involves course work, a qualifying examination, thesis work and a thesis examination, leading to the award of a PhD degree. Besides research, the scholars are involved in several activities such as helping the faculty as teaching assistants in theory courses and laboratory sessions. PhD students are also expected to participate actively in seminars, journal clubs, workshops, etc. There is considerable interaction amongst students at different levels and PhD students contribute significantly to mentoring fifth year MS students in research laboratories.

Students are required to pass a national level test, to be eligible for applying to the PhD program at IISER Mohali. Screening tests and interview are conducted to select the best students. Majority of doctoral students at IISER Mohali have qualified for fellowships given by CSIR, UGC, DST, DBT, ICMR and other agencies.

Admissions to the PhD program are carried out twice a year. Applications are invited in March and September of each year through an advertisement on the IISER Mohali webpages.

Doctoral graduates from IISER Mohali are doing post-doctoral research in some of the finest research groups in the world.