The school was first named Marikina High School – Concepcion Annex with Ms. Mary S. Dingcong as Officer-in-Charge, duly assigned by the then MHS principal, Ms. Lagrimas B. Garcia. It was situated outside the left and right wings of Concepcion Elementary School where two-story buildings were used as instructional classrooms .

Teachers from other annexes were added to the roster of faculty members of Marikina High School – Concepcion Annex, which was then relocated to J.P. Rizal Street, where it shared the campus with Tahong Elementary School. Assigned Officers-in-Charge were Ms. Myrna Antazo and Ms. Milanda Bautista, respectively. 

The school was officially named Concepcion Integrated School on May 15, 2002, by virtue of the City Council Resolution No. 067, Series of 2002, through the subsequent approval of the Department of Education, pursuant to DepEd Order No. 91, Series of 1999. This important milestone was realized through the untiring joint efforts of Mr. Rubi A. Parungao, the appointed principal of the Elementary Level at that time, and Ms. Lagrimas Garcia, principal of Marikina High School. 

The Division Office of Marikina City assigned Ms. Janet S. Amurao to CIS to manage both the elementary and secondary levels. It was this year when CIS produced its first batch of graduates. 

Significant developments took place in CIS. Physically, its once makeshift classrooms were turned into standard ones. Also, a nine-room extension funded by DPWH was put up. Internally, improvements in the school system took place, which included enhancements in the learner enrollment system, implementation of discipline, and engagement of stakeholders, among others. Teachers' welfare was also given emphasis through a more organized faculty club and the establishment of a teacher’s cooperative. 

The 20-classroom PAGCOR building was inaugurated and used by around 1880 learners and teachers.