When basic yoga poses and mindful self-regulation methods are interspersed in youth physical activity programming, mood might improve beyond that induced by exercise alone. Based on self-efficacy theory, mechanisms of mood improvements might include feelings of mastery over the exercise environment (i.e. exercise-related self-efficacy). A 45 minute/day physical activity component of elementary after-school care was administered either with basic yoga poses and methods of breath control and mindful self-regulation (treatment group, n=59), or in a traditional manner (comparison group, n=55) over a school year to boys and girls ages 9-12 years (mean age=9.9 years). Analyses of variance (ANOVAs) indicated that both overall negative mood and exercise self-efficacy improved significantly more over both the first half of the school year and full school year in the treatment group. Effect sizes increased over time. In mediation analyses computed separately over both temporal intervals, score changes in exercise self-efficacy significantly mediated the significant bivariate relationships between group and changes in negative mood. In further regression analyses, it was found that relationships between changes in mood and self-efficacy were reciprocal, and thus mutually reinforcing. Findings suggested a benefit of incorporating yoga and mindful self-regulatory skills into the physical activity components of children’s after-school care. They also supported self-efficacy theory, in that mood change was suggested to have occurred largely through treatment-associated changes in self-efficacy. Additional positive effects (e.g. on academic performance) of the inclusion of yoga and mindfulness strategies in youth physical activity programming should be evaluated in extensions of this research.