Professor Karandikar worked in Indian Space Research Organization, Ahmedabad between 1988-89. He was Member Technical Staff and Team Coordinator in High Performance Computing Group of Center for Development of Advanced Computing (C-DAC), Pune during 1994-97. Since 1997, he was working in the Department of Electrical Engineering of IIT Bombay as a Professor. He was also the Head of Computer Center of IIT Bombay during the period of 2008 to 2011 and the Head of the Department of Electrical Engineering from January 2012 to 4th January 2015.