Elementary school physical education can play a prominent role in promoting children's leisure-time physical activity. The trans-contextual model of motivation has been proven effective in describing the process through which school physical education can affect students' leisure-time physical activity. This model has been tested in secondary education, but there is no evidence on the applicability of the model in elementary education. In the present study, we assessed the effect of motivation in elementary school physical education on leisure-time physical activity motivation and the related decision-making process. The sample consisted of 241 pupils (M[subscript age] = 11.52, SD = 0.51) recruited from elementary schools in Northern Greece. Participants completed a questionnaire including measures of physical education and leisure-time physical activity motivational regulations, attitudes, subjective norms, perceived behavioral control, and intentions toward leisure-time physical activity. The results of hierarchical regression analyses indicated that motivational regulations in physical education best predicted the respective leisure-time physical activity regulations. In addition, leisure-time physical activity motivational regulations predicted intentions toward physical activity. Multiple mediation analyses indicated that the effect of leisure-time physical activity motivational regulations on intentions was partially mediated by perceived behavioral control. The findings support prior research and demonstrate an important mechanism of how motivation in elementary school physical education can influence leisure-time physical activity. Autonomous motivation in elementary school physical education led to higher students' intentions toward physical activity outside the school.