The institute is a joint venture of the Department of Atomic Energy (DAE) and the Kerala State Council for Science, Technology and Environment (KSCSTE).
Kerala School of Mathematics has a doctoral program to which students are admitted on an yearly basis.
The nascent plan to set up Kerala School of Mathematics started forming shape in around 2004.
The then DAE chairman Anil Kakodkar and the then executive vice president of KSCSTE, M. S. Valiathan were instrumental in setting up the institute with the guidance of M. S. Raghunathan, Rajeeva Karandikar and Alladi Sitaram.
The institute was later inaugurated in 2008 by the then Chief Minister V. S. Achuthanandan[3][4] and finally set up in 2009 with Parameswaran A. J. as the founding director.