This study investigates the role of Perceived Athletic Competence (PAC) and Health-Related Fitness (HRF) in mediating the reciprocal relationship between Motor Competence (MC) and Physical Activity (PA) during the transition from primary to secondary school. MC, PA, PAC and HRF were measured in 224 participants (baseline age 12.26 +/- .037 years; 51% female) in final year of primary school and one year later in first year of secondary school. Path analysis in AMOS 23 was used to test the mediating influence of PAC and HRF on the MC-PA relationship. Fit indices showed that, in both directions, HRF and PAC mediated the relationship between MC and PA (PA predicting MC; chi 2 = 3.91, p = .272, CFI = .99, RMSEA = .04. MC predicting PA: chi 2 = 6.46, p = .167, CFI = .99, RMSEA = .04). Pathways were stronger through HRF than through PAC, indicating that HRF is the more substantial mediator of the MC-PA relationship during the school transition. Pathways were stronger in the direction of PA predicting MC than in the reverse direction. Interventions seeking to influence PA and MC across the school transition should focus on HRF as it is a primary mediator of the MC-PA relationship.