School-based substance use prevention programs in the United States (U.S.) have traditionally emphasized primary prevention. Although widely implemented, many programs overlook students who are already using substances. The incorporation of secondary prevention strategies, including resource-oriented approaches, acknowledges the full spectrum of student experiences and may enhance the relevance and responsiveness of prevention curricula while advancing health equity. Such integration is particularly important given increasing concerns regarding youth mental health, polysubstance use, and barriers to treatment access. The objective of this review was to assess the integration of secondary prevention components within school-based substance use prevention programs. Following PRISMA-ScR guidelines, a systematic search of EBSCOHOST, PubMed, and Google Scholar was conducted in July 2025. Eligible studies included peer-reviewed articles published between 2000 and 2025 that evaluated U.S.-based middle and high school programs integrating resource-oriented strategies, such as harm reduction and help-seeking, during school hours. Non-U.S. programs, elementary school and college-based interventions, and grey literature were excluded. Among the twenty-four studies included, most (n = 16) focused primarily on prevention strategies such as refusal skills and substance use awareness, whereas eight studies incorporated resource-oriented elements, including harm reduction and help-seeking components. Theoretical grounding was inconsistent, with three studies lacking an explicit theoretical framework. Most programs were teacher-led and peer-enhanced (n = 18) and targeted universal student populations (n = 20). Few interventions were tailored to high-risk subgroups, such as adolescents with prior substance use, and cultural adaptation was uncommon. School-based substance use prevention programs commonly emphasize universal skills, normative education, and peer engagement approaches; however, several methodological limitations remain. Future research would benefit from more rigorous evaluation, clearer theoretical grounding, greater attention to cultural adaptation, and exploration of scalable, tiered hybrid models capable of supporting equitable and comprehensive prevention across diverse adolescent populations.