The school run for 25 years had to be closed down; the Sisters and the orphans were accommodated in Santhipuram Convent on the banks of Meenachil River.  The sisters took refuge at the intercession of St.Joseph, who had always been their patron at all times.  In 1922 their misery followed them in the form of flood, which overflowed the banks and the convent building was submerged in the flood.  Though a misery, this proved to be a blessing for the sisters. The Fathers of Good Shepherd Monastery gave refuge to the sisters and the orphans in Good Shepherd School and orphanage run by the Monastery.  The sisters and the teachers took over teaching the students of the school.  Soon the school became renowned and the strength increased as years passed.  Meanwhile, they purchased a land on the western side of the then M.C.Road opposite to the Good Shepherd School and constructed their convent and a primary school and orphanage for girls.
The school run at Good Shepherd was shifted  to the new building in.In 1924 the sisters were inducted to the CSST Congregation. Ever since St.Joseph School started in it had a name for itself for its excellence in character formation and academic performance.  Today thousands of young men and women are working all over the world, who had passed through the portals of St.Joseph. When we turn back to the pages of the school’s history we realize how much those responsible have contributed to this institution from its humble beginnings to its present progress and achievements of proud record.  All through these years it has stood as a beacon light dispelling darkness of illiteracy and instilling in the hearts of the young a thirst for truth, values, justice, love and service. Located at the heart of the town of Kottayam the School opened its doors with 57 students enrolled in kindergarten through eighth grade. Since its opening, the school’s dynamic educational environment  continued to evolve.  Soon after the school began, word started to spread.
In just three years, enrolment rose to 5 times.In 1981 the school was upgraded as a High School.  We had grown to offer all grades, from kindergarten through grade 10 excellent education and extra-curricular activities. Swamy Vivekanandan once said: “The education which does not help the common people to equip themselves for the struggle of life, which does not bring out strength of character, is not worth the name.  Real education is that enables one to stand on one’s legs.”  Therefore,  we had defined our Five Pillars, which include Academic Excellence, Personality Development and  Leadership, Talent Search and Promotion,  Artistic Excellence, and Community Action. Moving forward, the pillars helped ensure that students at every grade had opportunities to flourish and grow. We opened our boarding for  students in grades 9-12.
when we celebrated golden jubliee, a new  building was constructed with better facilities for class rooms, Laboratories, Library, indoor games, and computer labs.  In response to the COVID-19 pandemic, we opened in August of 2020 offering blended learning with on-site and virtual learning options for families. Throughout our history, the school community has remained committed to creating an environment in which students are known, supported, challenged, and encouraged to grow. Since the school – motto ‘excellence’ is all – inclusive of academic, aesthetic, athletic, spiritual, emotional, cultural and social dimensions of education, our students had been bringing coveted laurels to their school making it proud in every sphere of its educational venture.
The school has glorious innings and stands tall, set to soar higher towards perfection knowing that the sky is the limit.  The best is yet to come. During all these years of the progress of the school there have been struggles and pains, challenges and achievements as in  all human ventures.  However, God has always been with us in a tangible way and we gratefully acknowledge the marvels of His mercy, protection and blessings. We gratefully remember the Bishops and priests of  the Diocese of Vijayapuram for their timely help and guidance in our journey.
We experience all through the years a maternal care and love and encouragement from the CSST Congregation. The School PTA gives us strength and support.  The seminars we organize every year for the PTA members have proved to be excellent guidance in parenting. The Educational Department has always given us guidance and support in our academic as well as extracurricular activities. The support and fondling of the Corporate Educational Agency of the Diocese of Vijayapuram are such that We always felt safe and secure.