Purpose: The purpose of this pilot study was to evaluate the potential of an innovative high school neuroscience-based health course for implementation feasibility and impact on student outcomes. Methods: Thirteen teachers from two high schools participated in this quasi-experimental pilot study including 395 students (202 in the intervention classes and 193 in the comparison classes). Students completed pre/post online surveys assessing their knowledge, beliefs, and behaviors. Our analysis strategy for multi-item measures was to estimate the effects of the intervention on latent change scores in structural equation models (SEM). Results: Students in the neuroscience health classes showed a significant increase in neuroscience knowledge as compared to students in the comparison group (difference estimate in proportion correct metric, adjusted for covariates = 0.04; 95% CI [0.01, 0.06]). However, none of the other primary outcomes showed a significant difference between conditions. Teachers in the intervention group were observed implementing the neuroscience and health components more often than the self-regulation and growth mindset components. Students in the neuroscience group were more likely to mention the importance of caring for their brain and its link to health behaviors. Conclusions: Findings demonstrate that information about the link between health behaviors and brain functioning can be successfully integrated into a high school health education course, although effects on student health beliefs and behaviors were not observed. Additional development work should focus on clarifying the theoretical mechanisms of change, integrating the neuroscience content with self-regulation and growth mindset, and providing additional professional development for teachers.