St. Thomas School, Bahadurgarh  officially recognized the school in 1999, and in 2001, it obtained affiliation with the Central Board of Secondary Education. The inaugural batch of students graduated in 2003, marking the beginning of a series of successful results. St. Thomas School made significant achievements by securing both the 3rd and 6th ranks in the All India Secondary School Examination in a single year.

STS was a visionary project initiated by a young Keralite residing in the industrial town of Bahadurgarh, North India. Faced with the limitations of working under existing management systems and torn between providing opportunities to the privileged or the deserving, Mr. N. Thomaskutty, the eldest son of proud teachers, decided to establish a school based on his Christian ideals. Although the decision to start STS initially appeared impulsive, it eventually became evident that it was a manifestation of God's will in action.

The school had humble beginnings on April 6, 1995, within the residence of Prof. D.B. Malik. However, the estimated capacity of 150 students turned out to be a significant underestimation. In the very first year, the school had to accommodate 423 students. To overcome the space constraints, Mr. Prem Singh Parashar, a neighbor, selflessly offered his rented house for the school's use. The timely support and providence of these individuals played a crucial role in shaping STS into the success story it is today.

In 1996, the school managed to acquire land, and construction work commenced on August 24 of the same year. Following a dedication ceremony on September 18, 1997, the school relocated to its new premises, marking a significant milestone in its journey.