The time-worn elementary school buildings were replaced by two new buildings, which were constructed in 1991 and 1994 respectively. These were the five-storey structure topped by the multi-purpose Stephenian Hall; and the pre-school building topped on the fourth and fifth levels by the indoor gymnasium. These projects were the result of generous outpouring of financial support by alumni, Parish members and friends. In fact, the pre-school building project came about as a result of the continuous fund campaign that was started five years earlier (1990). A musical production entitled "Once Upon A Time" was staged as a fund-raiser at the Philippine International Convention Center in celebration of the school's 75th year in 1992.
The completed projects provided more rooms for additional facilities that further enhanced a well-rounded St. Stephen's education for the pupils. In 1993, the school became one of the founders of the 121-member Association of Chinese-Filipino schools in the Philippines and for one year, it housed the offices for the organization.
In December 1995, a landmark decision was reached that gave birth to the St. Stephen's High School Faculty and Staff Welfare Fund Foundation. The foundation was registered with the Securities and Exchange Commission (SEC). Again, the generosity of the alumni and friends of the school was tested and a successful fund drive yielded an initial Php 30 million realized target. On the occasion of the school's 80th anniversary, a concert entitled "The Sound of Stephenians" was held at the Cultural Center of the Philippines in November 1997. More donations were received. Thus, the school was finally able to begin extending medical benefits to the beneficiaries – the teachers and staff.
In 1998, Dr. Tiu Uy Pei Suan retired and Mrs. Joy Dy was named principal with Mrs. Judy Tan as assistant principal. Accredited Status Reconfirmed.
The upgrading of the school's facilities continued. A speech laboratory was set up and made possible by the School Board in 1999. The Jimmy Go swimming pool and facilities were constructed in 2001 and became a welcome part of the campus landscape. The Auditorium at St. Stephen's High School underwent major redesigning and renovation and was finally inaugurated in a festive program in November 2006. In the Summer of 2010, a multi-purpose hall in the high school building was put up in the former Science Lab area to better serve the students during lunch break.