System Thinking is an actual construct supported by several scientific evidence that offer a perspective on how phenomena relate. Rhythm methodology, teaching-learning, and enjoyment in physical education are the main system elements we hypothesize interacting closely to determine direct or mediated effects on motor creativity and rhythmic perceptive capacity. Seventy-six elementary and middle school students (8.9 ± 2.1 years) were randomly assigned to two groups: a) an intervention group that received a physical education lesson based on rhythmic methodology and b) a control group that received conventional lessons without specific rhythmic interventions. Participants were engaged in eight physical education lessons lasting one hour each for eight weeks. Tests and questionnaires were administered before and after the intervention to evaluate motor creativity, rhythmic perception capacity, self-perception and enjoyment. Two lessons were randomly analyzed to identify the teaching style and motor content (moderate and vigorous activity). The main results revealed direct effects on the intervention group’s motor creativity (p = 0.001) and its rhythmic perception capacity (p = 0.02). Furthermore, enjoyment mediated the effects of the intervention on motor creativity (p = 0.01). Finally, the results have shown that self-perception does not mediate the effect of rhythmic intervention group on motor creativity and rhythmic perceptive capacity (p > 0.05). A rhythmic methodology proposed by specific multi-teaching styles can involve children and young people in an enjoyable activity with more moderate to vigorous physical activity.