Since its founding, there have been changes in the Prajnya Board of Trustees.
Ratna Mukherjee, Sudha Ramachandran and Jaya Menon have left the Board of Trustees.
On January 4, 2009, Dr. D. Jayashree joined as a Prajnya Trustee. She is an Ayurvedic physician by profession.
Carnatic musician S.Sowmya was invited to join the Prajnya Board of Trustees on September 4, 2010.
The present composition of the Board of Trustees is Swarna Rajagopalan, Shilpa Anand, D.Jayashree and S.Sowmya.