Introduction: Physical activity (PA) decreases with age, and the transition from primary to secondary school is noted for significant changes in PA behaviours. Given the negative health outcomes associated with low PA this is a worrying trend. A conceptual model developed by Stodden et al. (2008) hypothesises a reciprocal relationship between PA and motor competence (MC) that is mediated by perceived competence (PC) and health-related fitness (HRF). This model has guided research in the PA domain, but to date, no longitudinal study has evaluated it in its entirety. The purpose of this thesis is to evaluate the model across the school transition to identify key pathways for positive PA behaviour. Method: Participants were measured at three timepoints (6th class primary: n = 261, 1st year: n = 299, and 2nd year: n = 108 secondary school. Baseline age = 12.22 ± 0.48 years). Measures at each timepoint included: PA (accelerometery), MC (five object-control skills, four locomotor skills, three balance skills), HRF (20m shuttle run test, horizontal jump, vertical jump, grip strength, push-ups, curl-ups, back-saver-sit-and-reach), and PC (perceived athletic competence, perceived physical appearance, global self-worth). Results: HRF was a stronger mediator than PC, and the MC-PA relationship was dominant in the direction of MC predicting PA. HRF was the strongest predictor of PA across the school transition. Changes in PA, MC, HRF and PC during the school transition were influenced by proximity to the transition, and differed between males and females. Conclusion: Findings partially support the pathways depicted in Stodden et al.’s (2008) model, particularly highlighting the importance of HRF as a mediator within the model, and as a predictor of future PA. Differences between males and females exist for some of the pathways, and for changes during the school transition.