Lesotho’s government has shown consistent efforts to implement social protection programmes. However, while recent evidence established a positive causal relationship between some of these programmes and food security there is little evidence on the extent to which these initiatives are associated with better educational and sexual and reproductive health outcomes among vulnerable adolescents in Lesotho. The study uses cross-sectional, nationally representative data from the 2018 Lesotho Violence Against Children and Youth Survey. Our research examined the association between social protection receipt and educational and sexual and reproductive health outcomes among adolescents and young people (13–24 years) living in poverty. We employed multivariate logistic regression controlling for age, orphanhood, HIV status and sex. Social protection receipt was defined as household receipt of financial support from a governmental, non-governmental, or community-based program that provides income. Additionally, we fitted a marginal effects model by sex. Among the 3,506 adolescent females and males living in the two lowest poverty quintiles, receipt of social protection was associated with improvements in multiple adolescent outcomes: higher odds of consistent condom use (aOR 1.64, 95% CI 1.17–2.29), educational attainment (aOR 1.79, 95% CI 1.36–2.36), and school enrolment (aOR 2.19, 95% CI 1.44–3.34). Stratified analyses by sex showed that social protection receipt was also associated with reduced likelihood of child marriage among females (aOR 0.59, 95% CI 0.42–0.83) and higher odds of educational attainment and school enrolment among males (aOR 2.53, 95% CI 1.59–4.03 and aOR 3.11, 95% CI 1.56–6.19, respectively). Our study provides evidence that social protection programs are associated with improved educational, sexual and reproductive health and child marriage prevention outcomes among adolescents living in poverty. Implementing and expanding such social protection initiatives could prove instrumental in improving the well-being of vulnerable adolescents.