Doctoral studies are offered by several of the Amrita Schools. In an era where knowledge creation and applied research is being acknowledged as the primary basis for the development and growth of society, Amrita aspires in the same direction, acknowledging the value of it. Doctoral Programmes are offered by the institution with a view to encourage aspiring scholars to take up research in the country.

The three Schools of Engineering offer programmes leading to the award of a Ph.D. degree in Engineering, Science and Humanities. The School of Medicine at Kochi offers a programme of study and research leading to a Ph.D. degree in various fields of medicine. The School of Biotechnology at Amritapuri, the School of Business at Coimbatore and the Center for Nanosciences at Kochi also offer programmes of study and research leading to the award of Ph.D. degrees.

Institution-wide, there are over 300 registered Ph.D. students. These include several members of the faculty who are pursuing their doctoral studies part-time, under the guidance of the senior Amrita faculty. Amrita has a pool of faculty with Doctorate from globally known Institutions and Universities who continuously engage in research. This has put Amrita in an advantageous position to initiate the Ph.D. programmes.

Amrita strongly believes in the dictum that knowledge grows when shared and thus encourages the faculty members to do so. In an endeavour to enrich their knowledge in contributing towards quality education, faculty members in all departments have been doing consistent research work. Many of the faculty members have contributed papers at the National and International venues. They regularly attend conferences to gain deeper understanding of their research areas.

A doctoral committee for each Ph.D. student at Amrita, comprising of a convener, thesis supervisor, thesis co-supervisor, and a faculty member from a minor area as needed, provides guidance and support. This committee recommends courses to be taken, convenes the oral exam committee, and monitors the progress of the student. Scholarship is provided to full-time Ph.D. students.