Remia H. Donguines, the school's founder, was appointed as the first principal of the newly instituted KES II.
KES II opened the school year in June 1999 with two regular classes/sections for each level from Kinder to Grade 6 and a Special Education (SpEd) class for visually impaired pupils.
The Sangguniang Barangay of Poblacion Kalibo and the Sangguniang Bayan of Kalibo endorsed a similar resolution supporting the move Finally, on July 26, 2011, Dr. Mildred L. Garay, Regional Director of the Department of Education, Region 6 acting for the Secretary of Education issued Government Recognition (RO VI) No.
KISEC has also positioned itself as the center of special education in the capital town of Kalibo and in the Province of Aklan while continuously producing graduates who have become successful professionals, board topnotchers, world-class athletes, artists, performers and contributing citizens of the country from its regular classes.
KISEC is supervised by the Department of Education under the District of Kalibo II, Division of Aklan, Region VI - Western Visayas.