The college has its beginnings in a primary school started at Kallai, near Calicut, in 1848 by the Basel Evangelical Mission with a strength of about 100 pupils in five classes. This was the first school to teach English in Calicut and the school was known as the B.G.E.M. Anglo- Vernacular School. In 1859, the school was shifted from Kallai to the heart of the town, east of Mananchira, where the B.E.M. Girl’s High School stands now. As years went by, the school became more and more popular and in 1872 it was raised to a middle school. Three years later, a new building was constructed for the school and subsequently, in 1878 the school was raised to a High School. Mr. G.T. Verghese was the first headmaster of the High School and under him, the school progressed rapidly.

The dawn of the twentieth century brought new challenges with the growth and expansion of the college. So in 1906, the school was shifted to the present building and the old building was handed over to B.E.M. Girl’s School. In 1909, the college got affiliation of the University of Madras, and as a Second Grade College, the first class was opened with fifteen students of whom four were women. The Rev. W. Mueller was the first Principal and the college was then called the Basel German Mission College. In the intermediate course, the subjects taught were English, Malayalam, Sanskrit, Kannada, Mathematics, Physics, Chemistry and Logic. Ancient History and Modern History were taught as the optional subjects. In 1928, Indian History was added and in 1929 German.

In 1911, when Rev. Mueller went on furlough, Mr. W.E. Hoare, M.A. (Oxon) was appointed Principal. On his return from furlough in 1915, Rev. Mueller resumed office as Principal. In the following year, Mr. Hoare was again appointed Principal. During his tenure, a hostel to accommodate fifty students was constructed near the college. Within three or four years of the starting of the college, it was decided to raise the college to the first-grade level and plans were prepared for more buildings. However, the upgradation and expansion plans suffered a setback when the German missionaries were recalled with the outbreak of World War I and the Home Board of the Basel Mission withdrew its missionaries from Malabar in 1919.

The Madras Christian College took over the Management of the College and its name was then changed to Malabar Christian College. In 1920, Mr. Hoare retired and Mr. Joseph Muliyill, B.A. from Madras Christian College, was appointed Principal. In the following year, Mr. Muliyill went back to Madras Christian College, and Mr. Askwith M.A. (Cantab) was appointed Principal. In 1927, the college was again taken over by the Basel Mission and Rev. A. Muench took over the charge as Principal and continued till Rev. A. Streckeisen succeeded him in 1930. During 1934, Father of our Nation, Mahatma Gandhi visited and blessed the institution. In 1935,Rev. Streckeisen was succeeded by Dr. F. Melzor. After serving for two years, Dr. Melzor left to take up evangelistic work and Dr.T.H.Lorch was appointed Principal. Dr. Lorch made several improvements in the college. His determined effort to upgrade the college were once again foiled with the outbreak of World War II and this brought an end to his term. In 1939, Mr. J.F. Thaddeaussucceeded Dr. Lorch. In 1940, the Basel Mission transferred the management of the college and school to the Malabar and South Canara Christian Education Society registered under the Societies Registration Act of 1860.

Dr. V.G.M. Pavamani assumed charge as Principal in June 1953. Under his stewardship, B.A. Economics and B.Sc. Mathematics courses were started and the college bloomed into a first-grade college in July 1956. In 1957, B.Sc. Degree Course in Chemistry, Physics and Zoology was introduced. In 1964, the two-year Pre-Degree course was introduced in place of the one-year Pre-University course. The college commenced its first Post Graduate course, M.Sc. Zoology in 1965. In 1967, he was succeeded by Mrs. V.G. Lancelot Thomas.

Consequent on the formation of the University of Calicut in July 1968, the college was affiliated to the University of Calicut. The Home Board of the Basel Mission transferred the Management to Malabar Christian College to the Interim College Council set up by the Interim Diocesan Administrative Committee of the North Kerala Diocese of the Church of South India. This caused court case. Due to this, three Government College Principals, Prof. M.C. Krishnan Nambiar, Dr. V. GovindaShenoy and Prof. K.N. Balakrishnan Nair were in charge of the college on deputation.

In 1972, Dr. A.J.Hermon was elected unanimously as the first Manager of the College. In 1979, Dr. A. Yesuratnam was appointed as Principal. In 1980, shift system was introduced. In 1980-81, B.A. Course in Malayalam started. On 31.03.1982, the new management, viz. North Kerala Diocese of C.S.I., took charge.

In 1988, Rev. Dr. Samuel Coodacal was appointed as Manager of the College, Dr. Yesuratnam retired on 31.03.1989 and was succeeded by Prof. P.P.Skaria, who retired on 31.03.1990. He was succeeded by Dr. Clement Adolph. He brought about many changes in the infrastructure of the college, but died in harness on 27.11.1990. He was succeeded by Prof. V.M.N. Namboodiripad for a short span of six months after which, Dr. Viola Irene Hunt assumed charge as the Principal in 1991. The New Block was constructed in 1994 and consequently, the shift system was abolished. During her tenure, the M.A. Course in History was started in 1995.

Prof. Christhakumar W.E. Nicholas became the Principal in 1997. During his tenure, three new courses were started – the B.A. Functional English (1998), M.Sc. Chemistry (1999) and M.A. Malayalam (2001). Malabar Christian College was selected for the State Award for the best NSS Unit of the year 1997-98. Prof. Merlyn Premdas was appointed Principal on 18.10.2002. She initiated the process for UGC-NAAC accreditation.

Prof. Gladys P.E. Issac took over as Principal on 31.03.2004. During her tenure, the college witnessed its yearlong centenary celebrations and the two National Assessment and Accreditation Council (NAAC) visits. The college was accredited with a B+ Grade in the first visit in 2004 and with an A Grade (CGPA 3.21) in the second visit in 2012. An Audio Visual Theatre was built and donated to the college by the staff to commemorate the occasion of the centenary celebrations. In 2013, Prof. Pavamani Mary Gladys succeeded Prof. Gladys and during her tenure, eight courses were started. The courses are B.Com. (Finance) and M.Sc. Mathematics in 2013; Self- Financing courses viz. M.Sc. Physics, M.A. English Literature and M.A. Economics in 2014; and the Self-Financing courses viz. B.Com with CA, BBA and MCJ in 2015. The DCA Programme in collaboration with Government of Kerala (CCEK) and the SIDCO CCEK one-year course in Engineering Theory was also introduced during 2014-15. The Department of Malayalam and History became Research Departments in 2013 and 2015 respectively. A New Academic Block was constructed in October 2014 under the supervision of the Manager Rev. Dr. T.I. James. The present Manager, Mr. Jayapal Samuel Zachai succeeded Rev. James in 2014.

Prof. Pavamani Mary Gladys was succeeded by Dr. Godwin Samraj D.P. who assumed charge on 19.09.2016. In his tenure, the Research Block, the DST-FIST Network Centre and the renovated Chemistry Department are unveiled and blessed by the Bishop Rt. Rev.Dr. Royce Manoj Victor on 23.09.2016. Dr. ME Premanand of the department of English was awarded with the Prof. MM Ghani award for Best Teacher by the University of Calicut in 2017. The new indoor sports facility was unveiled and blessed by Bishop Rt. Rev. Dr. Royce Manoj Victor on 22.03.2018. The construction of a new audio visual hall was completed in the year 2021 with the financial aid from RUSA. 

Dr. Sachin  P James took temporary charge of the Principal on 04.01.2022 as Dr. Godwin Samraj completed his tenure.