Filipino students performed poorly in the 2018 Programme for International Student Assessment (PISA) mathematics assessment, with more than 50% obtaining scores below the lowest proficiency level. Students from public schools also performed worse compared to their private school counterparts. We used machine learning approaches, specifically binary classification methods, to model the variables that best identified the poor performing students (below Level 1) vs. better performing students (Levels 1 to 6) using the PISA data from a nationally representative sample of 15-year-old Filipino students. We analyzed data from students in private and public schools separately. Several binary classification methods were applied, and the best classification model for both private and public school groups was the Random Forest classifier. The ten variables with the highest impact on the model were identified for the private and public school groups. Five variables were similarly important in the private and public school models. However, there were other distinct variables that relate to students' motivations, family and school experiences that were important in identifying the poor performing students in each school type. The results are discussed in relation to the social and social cognitive experiences of students that relate to socioeconomic contexts that differ between public and private schools.