Parochial schools are assumed to provide better social and academic experiences; however, few studies account for selection bias when comparing with public schools. This study contrasted public versus parochial schools using propensity score matching across a range of outcomes (e.g., perceptions of school, emotional symptoms, substance use, bullying). Using a sample of 58 public and 5 parochial high schools, the nonmatched analyses suggested a significant advantage for parochial schools students (e.g., better on 23 of 32 indicators). However, the propensity score matched analyses revealed nine differences (e.g., weapon carrying, smoking), two of which (i.e., stress and cyberbullying) favored public schools. While at first glance parochial schools generally appear to be healthier and safer learning environments, accounting for selection bias, the gap was narrowed. Students in parochial schools may struggle with issues related to social, emotional, and behavioral health risk, and thus prevention programs should also be implemented in these settings.