Risk and protective factors play crucial roles in shaping problem behavior, substance use, and mental health outcomes among adolescents. The study aims to examine the risk and protective factors and their association with emotional and behavioral problems among school-going tribal adolescents in Meghalaya, India. This study employed a cross-sectional design, utilizing a simple random sampling method to select schools from the Ri-Bhoi district (Nongpoh town) and East Khasi Hills district (Shillong cantonment area) of Meghalaya. A total of 450 students participated in the survey, out of which 300 students belonged to tribal ethnicity. The study focused on school-going adolescents with tribal ethnicity, aged 13-19 years, encompassing both genders (male and female). Participation in the study required both parental consent and the adolescent's assent. The Communities That Care Youth Survey (CTC-YS) and the Strength and Difficulty Questionnaires (SDQ), scale were administered. The findings highlighted significant risk factors including laws and norms favorable to drug use, community disorganization, poor family management, and low school commitment. Protective factors such as opportunities for prosocial involvement were evident across all domains. Family conflict, family history of antisocial behavior, and parental overcontrol were significant contributors (P < 0.05) to total difficulty scores. Among individual risk factors, "Interaction with anti-social peers" (P = 0.009) and "Intentions to use substance" (P = 0.021) had significant associations with higher difficulty scores. The overall prevalence of mental health problems, as indicated by the total difficulty score, was 31.3% among school-going tribal adolescents. The high prevalence of mental health problems, especially among tribal adolescents, underscores the urgent need for targeted interventions. By addressing these factors, policymakers and stakeholders can work toward fostering healthier outcomes for tribal adolescents in Meghalaya and similar communities.