The purpose of the present study was to directly compare the acute effects of participating in a single yoga class versus a single standard physical education (PE) class on student mood. Forty-seven high school students completed self-report questionnaires assessing mood and affect immediately before and after participating in a single yoga class and a single PE class one week later. Data were analyzed using paired-samples t tests and Wilcoxon-signed ranks tests and by comparing effect sizes between the two conditions. Participants reported significantly greater decreases in anger, depression, and fatigue from before to after participating in yoga compared to PE. Significant reductions in negative affect occurred after yoga but not after PE; however, the changes were not significantly different between conditions. In addition, after participating in both yoga and PE, participants reported significant decreases in confusion and tension, with no significant difference between groups. Results suggest that school-based yoga may provide unique benefits for students above and beyond participation in PE. Future research should continue to elucidate the distinct psychological and physiological effects of participating in yoga compared to PE activities.