Socioeconomically disadvantaged populations are at greater risk of adopting unhealthy behaviours and developing chronic diseases. Adolescence has been identified as a crucial life stage to develop lifelong healthy behaviours, with schools often suggested as the ideal environment to foster healthy habits. Health literacy (HL) provides a possible solution to promote such healthy behaviours. The aim of this study was to review school-based HL-related interventions targeting socioeconomically disadvantaged adolescents and to identify effective intervention strategies for this population. Searches were performed in six databases. Inclusion criteria included age: 12–16; the implementation of a school-based intervention related to HL aimed at socioeconomically disadvantaged populations; an intervention focused on: physical activity (PA), diet, mental health, substance abuse or sleep. Forty-one articles were included, with the majority focusing on PA and diet (n = 13), PA (n = 9) or mental health (n = 7). Few interventions focused solely on substance abuse (n = 2) or sleep (n = 1), and none targeted or assessed HL as an outcome measure. There was huge heterogeneity in study design, outcomes measures and effectiveness reported. Effective intervention strategies were identified that can be used to guide future interventions, including practical learning activities, peer support and approaches targeting the school environment, the parents or that link the intervention to the community.