Running under the tutelage and leadership of the Brothers of Holy Cross, a Roman Catholic Religious Congregation dedicated and committed to promoting education among the common masses, the present St. Joseph Higher Secondary School saw the light of the day on 19 March, 1954 as St. Joseph High School at 16, Monir Hossain Lane, Narinda, the heart of the then Dhaka City, with only four students. The school was founded by the late Brother Jude Costello, C.S.C. who was then the Headmaster of St. Gregory's High School. As the Headmaster of the school or a short time since its inception, he steered the school to a considerable expansion. The steady increase in the number of students in the following years expedited the necessity of shifting the school to a conveniently larger site at 32, Shah Sahib Lane at Narinda. The late Brother Jude Castello, C.S.C., a great scholar and exponent of educational expansion, acquired property for the school in Mohammadpur area.

He was soon taken over by Brother Fulgence Dougherty, C.S.C. who shouldered the responsibility to erect buildings in the new site at Asad Gate. Later on, Brother Gerald Kraeger took over the duties and responsibilities of the Headmaster and carried the remaining work through. The ease of access to Mohammadpur, the big playground and the steady progress of skilled workmen drew the attention of the student community of Dhaka city. And eventually the school was shifted to its newly-built campus at 97 Asad Avenue, Mohammadpur, Dhaka 1207 in 1965.

Initially, the school was an English Medium International School following the syllabus and curriculum of the University of Cambridge. But in accordance with the decision of the Government, the school was transformed into a Bengali Medium Secondary School in 1972 under the Board of Intermediate and Secondary Education, Dhaka.

Brother John Rozario, C.S.C., a legendary Principal of St. Joseph Higher Secondary School during 1990-2007, now acting as the Emeritus Principal, conceived the idea of transforming the secondary school into a Higher Secondary School. He made great strides in promoting the school to college level. Under his leadership and patronage, the school ventured to open the College Section with an English version Science Section in 1999 and turned out to be a great success in the very first year of Board Exams. In 2001 Bengali version Science Sections and Business Studies Section and in 2004 Humanities Section were added for further extension of the institution.

Bro. John Rozario C.S.C also initiated an English version (NCTB Curriculum) Section of Class-VI in 2004. Now the school section has three sections in each class, of which one is the English version.