Pazhassiraja College was established in 1982 in the picturesque Wonderland of Wayanad District of Kerala, situated on the eastern slopes of the Western Ghats. The college is affiliated with the University of Calicut and was founded by the 'Pazhassiraja Education Society', which was formed to cater to the needs of the local people in higher education. The founder and manager of the college is the late T.U. Jacob, the then president of the society. The college began operations on October 20, 1982.

Wayanad is a remotely situated tribal district in Kerala. The population includes mainly the settlers who migrated from the lowlands of Kerala and the native tribal people. Their main source of revenue is from agricultural produce such as pepper, coffee, paddy, etc., and the children of this highland did not have higher education facilities in the district until the first college was started here in 1964. The college had a humble beginning on October 20, 1982, with two pre-degree batches. The early days of the college were miserable. Fighting against all odds, the college started with only 127 students, 7 teachers, 8 office staff, and the first principal, Dr. O. Sooryanaryanan, who came from Government Brennen College, Thalassery. The society struggled a lot to get suitable land for this college, and finally, they bought this piece of land of about fifteen acres, just 1.5 kilometers away from the zero point of Pulpally.

In July 1992, the management of Pazhassiraja College was transferred to the Malankara Catholic Diocese of Bathery. The fast development of the college owes much to the foresighted vision of the late Bishop Dr. Cyril Mar Baselios, the then manager and patron of the college, the first bishop of the diocese, and the first major archbishop and Catholicos of the Malankara Catholic Church. In 1995, His Excellency Dr. Geevarghese Mar Divannasios became the manager and patron of the college. In 2010, His Excellency Dr. Joseph Mar Thomas became the manager and patron of the college, and the college continues its cherished journey of higher education today under his able leadership and patronage. In 1992, the college acquired minority status by the rights of the minority community granted in the Indian Constitution.

Though a minority institution, the college includes in its purview the educational aspirations of society as a whole, irrespective of religion, caste, gender, and social status. The institution seeks to foster equitable social development through the empowerment of individuals who can contribute to the common good. As a result, they become aware of their role in social reconstruction. The college tries to facilitate and encourage higher education among people who have been denied such opportunities because of socioeconomic backwardness.

In 1990, the college was upgraded when the Government. of Kerala sanctioned the first undergraduate course in economics. Subsequently, other courses such as B.A. History (1993), B.A. Travel and Tourism Management (1995), BBA (1998), and B.Sc. Microbiology (1999). B.Sc. Biochemistry (2002), M.Sc.Microbiology (2002), Master of Travel & Tourism Management, B.A. Mass Communication (2005), B.A. English Literature (2013), M.Sc. Biochemistry (2013), MCJ (2013), M.A. Economics (2014), M.Com. (2014), B.Voc Food Science and B.Voc Agriculture (2018), and BA Econometrics and Data Management (2021) were sanctioned, and at present Pazhassiraja College is a first-grade college with eleven UG and six PG programs. In 2015, Pazhassiraja College was accredited with a B grade by the National Assessment and Accreditation Council (NAAC). In 2022, Pazhassiraja College was reaccredited with an A+ grade by the NAAC.