Substance use among youth is a significant health concern in the rural United States, particularly among at-risk students. While evidence-based programs are available, literature suggests that an underdeveloped rural health prevention workforce often limits the adoption of such programs. Additionally, population-size restrictions of national mentoring programs can hinder their adoption in rural areas. This study sought to determine the effectiveness of a school-based group-matched mentoring program on at-risk students in two rural Missouri school districts using an intervention-control group design. At-risk students (n = 65) identified by school officials participated in a school-based mentoring program (One Life) designed to reduce substance use and impact social ecological risk factors. Compared to controls (n = 29), participants indicated reductions in 30-day use of tobacco (p = 0.037), alcohol (p = 0.001), and inhalants (p < 0.001). Additional benefits included increased interest in higher education and improved skills in peer development (p < 0.05). Social ecological mentoring can be a viable option for school-based drug prevention programs targeting at-risk rural youth.