This study explores the education inequality brought about by senior high school (SHS) choice of families in Bongao, Tawi-Tawi, Philippines, considering a nonmonetary approach to social class based on parental occupation. Furthermore, it underscores implications for educational public-private partnership (EPPP) regarding the K-12 SHS Voucher Program in the Bangsamoro Autonomous Region in Muslim Mindanao (BARMM). We used the explanatory sequential mixed methods research design, wherein quantitative research is complemented by qualitative research. A survey of family education, parental (breadwinner) occupation, and SHS school choice was conducted among Grade 12 public, private, and charter schools students. Data analysis considered social status, power of school choice, and the Autonomous Region in Muslim Mindanao (ARMM) government. Results showed more SHS participation from the middle class. Although the charter SHS entails social cohesion, overall findings suggest student segregation in the municipality, considering the public and private SHSs student compositions. As such, there is education inefficiency and inequity, revealing EPPP inefficiency. Based on document analysis, a complementary method, these education inequality issues are attributed to the partial implementation of ARMM regional autonomy posing constraints to government service delivery and compounding poverty. Therefore, government support and regional mechanisms to strengthen capability and accountability are recommended to enhance the state capacity and service delivery in BARMM, Philippines.