Background: Adolescence is a critical period of human development, however, limited research on programs to improve health and well-being among younger adolescents living in conflict-affected and humanitarian settings exists. The purpose of this study was to assess the comparative effectiveness of an economic empowerment program on young adolescent outcomes in a complex humanitarian setting. Methods: This longitudinal, mixed methods study examined the relative effectiveness of an integrated parent (Pigs for Peace, PFP) and young adolescent (Rabbits for Resilience, RFR) animal microfinance/asset transfer program (RFR + PFP) on adolescent outcomes of asset building, school attendance, mental health, experienced stigma, and food security compared to RFR only and PFP only over 24 months. A sub-sample of young adolescents completed in-depth qualitative interviews on the benefits and challenges of participating in RFR. Results: Five hundred forty-two young adolescents (10-15 years) participated in three groups: RFR + PFP (N = 178), RFR only (N = 187), PFP only (N = 177). 501 (92.4%) completed baseline surveys, with 81.7% (n = 442) retention at endline. The group by time interaction (24 months) was significant for adolescent asset building (X 2 = 16.54, p = .002), school attendance (X 2 = 12.33, p = .015), and prosocial behavior (X 2 = 10.56, p = .032). RFR + PFP (ES = 0.31, ES = 0.38) and RFR only (ES-0.39, ES = 0.14) adolescents had greater improvement in asset building and prosocial behavior compared to PFP only, respectively. The odds of missing two or more days of school in the past month were 78.4% lower in RFR only and 45.1% lower in RFR + PFP compared to PFP only. No differences between groups in change over time were found for internalizing behaviors, experienced stigma, or food security. Differences by age and gender were observed in asset building, prosocial behavior, school attendance, experienced stigma, and food security. The voices of young adolescents identified the benefits of the RFR program through their ability to pay for school fees, help their families meet basic needs, and the respect they gained from family and community. Challenges included death of rabbits and potential conflict within the household on how to use the rabbit asset. Conclusion: These findings underscore the potential for integrating economic empowerment programs with both parents and young adolescents to improve economic, educational, and health outcomes for young adolescents growing up in rural and complex humanitarian settings. Trial registration: NCT02008695. Retrospectively registered