St. John's College, Agra, was established in 1850 by the Church Missionary Society of England through the efforts of the Agra C.M.S. Association which came into being in 1840. The first Principal of the College The Rev. Thomas Valpy French, a distinguished fellow of University College, Oxford, was a man of great vision and missionary zeal. At its inception, the College formulated its own curriculum and conducted its own examination. From 1862 to 1888 the College remained affiliated to Calcutta University and later up to 1927 to Allahabad University. In 1927 with the formation of Agra University, the then Principal of the College Dr. A.W. Davies became its first Vice-Chancellor and the College was affiliated to the Agra University.
The College from its beginning strived for extension of education keeping dispensation of social justice through education and upliftment of the downtrodden as one of its major concerns. The first scheduled caste student was admitted as early as 1892 not withstanding considerable opposition from many influential quarters of those years. The college became a First Grade College in 1891 with B.A. and LL. B. classes, and affiliation was granted in 1893 for postgraduate classes. Thus it has the rare distinction of being a postgraduate institution of more than a century's standing.
The College can boast of having one of the most beautiful buildings in North India, built in red sandstone in Indo-Saracenic architecture. The foundation stone of the Centenary Wing was laid by Bharat Ratna Sarvapalli Radhakrishnan, former President of India, in 1958 and was opened by Bharat Ratna Pt. Jawaharlal Nehru, the first Prime Minister of India, in 1959, with the words "I have come to pay tribute to this temple of learning." The College has very distinguished alumni, the foremost of them being the late Dr. Shanker Dayal Sharma, the former President of India.