The prevalence of psychological distress is increasing in the Philippines, a country with limited resources for mental health programs. It is worthy to investigate the possible predictors for psychological distress among Filipino youth as they are one of the vulnerable populations to psychological distress. The present study aimed to explore the school-based mental health programs, protective factors, and psychosocial factors associated with psychological distress among Filipino school-going adolescents. This study analyzed the 2019 Philippine Global School-based Health Survey, which involved 10,175 high school-going adolescents. Logistic regression was used to determine factors associated with psychological distress (loneliness, anxiety, suicidal ideation, plan or attempt). Results indicate that almost three out of every 10 (27.8%) Filipino school-going adolescents reported experiencing psychological distress. In the adjusted model, having been taught about depression and suicide, taught what to do if a friend is suicidal, current alcohol use, current drug use, sedentary behavior, bullying victimization, and physically attacked were positively associated with psychological distress. Conversely, male sex, attending a public school, parental understanding, and having close friends were negatively associated with psychological distress. Psychological distress among Filipino school-going adolescents has nearly doubled since 2015. School-based mental health programs including suicidal content, demographic and psychosocial factors increased the likelihood of psychological distress and protective factors and having been taught about stress management decreased the odds of psychological distress.