When Mr. Chien Yin Shao retired in 1994, Mrs. Joan Sy-Cotio was designated by the Board of Trustees as Acting President. Seven months later, she was appointed to lead the institution as the College President.

During the school year 1997-1998, the Commission on Higher Education (CHED) granted CKSC the permit to operate The Faculty of Graduate Studies (FGS) offering Master of Arts in Education (M.A. Ed.) major in Administration and Supervision, Teaching and Computer Education, and Master in Business Administration (MBA). By the second semester of the same school year, the construction of a 10-story college building in Narra St. started.

In October, 1999, the new college building at Narra St., was inaugurated with no other than the former Vice President Gloria M. Arroyo as the inaugural guest. It was finally occupied by the FBAS and FGS. The permit to offer Bachelor of Science in Information Technology (BSIT) and Bachelor of Science in Information Management (BSIM) was granted by CHED during the Academic Year 2000-2001. These two programs were granted Recognition by CHED in June, 2002.

In September 2003, the Board of Trustees passed a resolution to operate the Bachelor of Science in Nursing (BSN) program. In view of this, the School of Nursing was opened during the school year 2004-2005. In the same academic year, The School of Teacher offered Teaching Chinese as a Second Language, major in the Bachelor of Secondary Education (BSE) program. This new major is offered in consortium with the Fujian Normal University, Fuzhou, China.