The earliest mention of this college is January 15, 1885. This began as a small parochial school for the boys of the Cathedral parish located first in a rented house. The foundation stone of the nucleus of the present building was laid by Rt. Rev. Dr. Peschi in 1884. Bishop Poli called this little primary school St. Joseph's Collegiate. In 1887 it was recognized as a middle school; it was recognized as "European High School" affiliated to Cambridge University. In 1907, it came directly under the Bishop and the Parish Priest of the Cathedral. It was handed over to the Christian Brothers of Nainital in 1908 and they looked after it till 1916 when Bishop Gramigna took it over. With a boarding of 26 students the total went up to 63 in 1920.

Another storey was put up in 1922 by Rev. Fr. Camillus, OFM Cap. The coming of a new Head Master in 1921 in the person of Msgr. O. Hogan who, graduated from the Allahabad University and trained in Oxford, put the School on the top of academic results. In 1984, St. Joseph's College celebrated its centenary. The college has updated itself according to the times and is excelling now both academically and extra-academically.