Meaningfully engaging and supporting youth in their communities can promote their sense of efficacy and potentially their health and wellbeing. The objective of this study was to test whether a school-based youth civic empowerment program, Generation Citizen (GC), was associated with self-reported mental and physical health among participants, and whether these associations differed by two potential modifiers: civic self-efficacy and a sense of meaningful contributions to one's community. Participants were middle and high school students (N = 364) who participated in GC in the fall semester of 2014 and completed surveys at the beginning and end of the semester. Analyses revealed a small but statistically significant increase in self-reported physical health after GC and no statistically significant change in self-reported mental health. There was evidence of effect measure modification by civic self-efficacy such that the difference in physical health as civic self-efficacy increased was smaller post-intervention compared to pre-intervention. This could suggest that GC participation is particularly beneficial for those with lower civic self-efficacy. While our findings suggest that public health interventions may benefit from centering empowerment opportunities for youth, future research is warranted to better understand the particular role of civic self-efficacy in that process.