The Carmelite Missionaries started this school in 1857 in the building which is at present the AG's office, Trivandrum. Later it was shifted to the campus near to St.Joseph's Cathedral, Palayam. In 1905, the school was again shifted to its present location near the General Hospital, Trivandrum. Sri.Madhava Rao, the then Dewan of the erstwhile Travancore declared St.Joseph's as a recognized school of the Travancore State at a public meeting held at the school campus on 18th January 1905. The school continued to function under the patronage of the Carmelite Missionaries till 1946. St. Joseph's came under the direct patronage of the Diocese of Trivandrum when His Excellency Rt. Rev. Dr.Vincent Derriere OCD took over the management as the first Bishop of the newly erected Diocese.

The Diocese invited the Salesian Fathers in 1946 and gave the management of the school to them. Once they completed their term, they returned the administration of the school to the diocese in 1952. The diocese directly managed the school for sometime and later the diocese invited the Jesuit Fathers, the pioneers of the qualitative education, to take over the management of the school in 1961. 'MAGIS' was their motto and they brought the school to its glory and was ranked as a prime institution in the capital city of God's Own Country. Once they completed their mission of MAGIS, they gratefully returned the management back to the diocese in 1998.
His Grace Most Rev. Dr.Soosa Pakiam M., alumnus of this great Alma Mater took over the management of this great institution in 1998 as it's Patron.

2004-05 was the centennial of this great Alma Mater of thousands and thousands of excelling personalities in all walks of life. 'Diligence Brings Excellence' was the slogan of the centenary celebrations.