The study determined and described the intended and the implemented curriculum of Special Science High Schools in South Central Mindanao, Philippines towards policy recommendations to address the gaps. Specifically, it determined the levels of implementation of curriculum, instructional programs, and instructional support. Both quantitative and qualitative data were employed in the study for collecting and analyzing the data. Specifically, it utilized multiplecase analysis. Triangulation procedure was used in collecting data through questionnaire, interview, documents and on-site visitation. The quantitative data established which areas have gaps while the qualitative works on description and judgment to identify what created them. The result of the study showed that there are significant gaps between the intended and the implemented curriculum in some areas of curriculum implementation, instructional programs, and instructional support. Policies cited in the Department of Education Orders are not generally implemented in all science high schools investigated.