H.H. The Rajah’s College, which was first established in the year 1857, as Maharajah’s Free English Medium School, has now attained the state of an esteemed institution with real potential for excellence. This school, under the first Headmastership of one B.T., Assistant nomination was started by the Thondaiman Kings in the erstwhile Princely State of Pudukkottai in 1879. The Free English Medium School started functioning in 1879 in a spare building at Vadakku Raja (North Main) Street in Pudukkottai. The first batch of the final year students of this school were sent for the terminal exam to the Madras University in 1880. Hence, 1880 is considered as the starting year of this College. The College celebrated its centenary year in 1982 and its 125th year in 2006.

In 1891, the high school classes and the college classes were transferred to the present building. The Head Master of the Maharajah Free English Medium School Mr. S. Narayanaswamy Ayyar B.A., was appointed as the first Principal of this College.
A sum of Rupees Two Lakhs was spent for building the compound wall around the college playground. From the academic year 1989-1990, M.Phil Course was offered in both Commerce and History. Thus, the college reached yet another glorious milestone in its pursuit of growth and development. Later, M.A. Economics and B.Sc. Physical Education courses were started during 1990 - 1991. Ph.D. Full Time course was introduced in the Department of History during 1992-1993. B.Sc. Computer Science was started in 1996. The College was declared as an Autonomous College by the University Grants Commission in its letter dated 05.10.1998, during the Academic year 1998-99. The College was awarded with the 3 Star Status by the National Assessment and Accreditation Council (NAAC) during 1999-2000. Later, B+ status was granted by NAAC to the college on 06/02/2006.