The academic course programs (BTech/MTech/MSc) are the responsibility of individual departments, which will also run minor streams in some cases. The research specific to disciplines that are part of the department shall also be conducted therein. The thematic interdisciplinary research centres have a major focus on research and will also run MTech programs and offer minor courses/electives for BTech programs. The departments/centres at IIT Palakkad with the corresponding heads are as follows.

• Department of Biological Sciences and Engineering
  • Prof. Jagadeesh Bayry, hodbse@iitpkd.ac.in | 9188952142
• Department of Chemistry
  • Dr. Dinesh Jagadeesan, hodcy@iitpkd.ac.in | 9188952143
• Department of Civil Engineering
  • Dr. M. V. Anil Kumar, hodce@iitpkd.ac.in | 9188952144
• Department of Computer Science and Engineering
  • Dr. Jasine Babu, hodcs@iitpkd.ac.in | 9188952145
• Department of Data Science
  • Dr. Narayanan C Krishnan, hodds@iitpkd.ac.in | 9188952146
• Department of Electrical Engineering
  • Dr. Mahesh R Panicker, hodee@iitpkd.ac.in | 9188952147
• Environmental Sciences and Sustainable Engineering Centre
  • Dr. Deepak Jaiswal, hocess@iitpkd.ac.in | 9188952148
• Department of Humanities and Social Sciences
  • Dr. Reenu Punnoose, hodhss@iitpkd.ac.in | 9188952149
• Department of Mathematics
  • Dr. M. Ashok Kumar, hodma@iitpkd.ac.in | 9188952150
• Department of Mechanical Engineering
  • Dr. Samarjeet Chanda, hodme@iitpkd.ac.in | 9188952151
• Department of Physics
  • Dr. Jayakumar Balakrishnan, hodph@iitpkd.ac.in | 9188952152

The distinguishing features of the  academic administration at IIT Palakkad are the following.

• Faculty members are allowed to hold multiple affiliations
• Graduate research programs (MS/PhD) are administered centrally by the Graduate Research Council.

The structure hinges on the philosophy of freedom and mobility of faculty members and students across different departments/centres with the research student administration and research infrastructure being opaque to these departments/centres. Every faculty member will have a primary affiliation, with either a department or an interdisciplinary research centre, and can have a secondary affiliation in another department or interdisciplinary centre. Faculty members who have a primary affiliation with a centre must necessarily have a secondary affiliation with a department. It is possible for faculty members to change or add to their affiliation any time during their career.

The Head of Department (HoD), appointed for a term of three years, will be the chairperson of the Departmental Consultative Committee (DCC) and will provide guidance to the faculty on teaching, research and administration.  The Head of the Centre (HoC), who is appointed for a term of five years, will administer the research and teaching activities with the help of the Centre Consultative Committee (CCC).