© 2020 by the authors. Licensee MDPI, Basel, Switzerland. Physical activity (PA) decreases with age. The school transition is noted for significant changes in PA behaviour. Motor competence (MC), health-related fitness (HRF), and perceived competence (PC) are generally positively associated with PA. The aim of this study was to examine longitudinal cross-lagged relationships between PA, MC, HRF, and PC across the school transition from final year of primary school to first year of second-level school in Irish youth. PA (accelerometery), object-control and locomotor MC (TGMD-III), PC (perceived athletic competence subscale of the Self-Perception Profile for Adolescents), and HRF (20 m shuttle run, horizontal jump, vertical jump, push-ups, curl-ups) were measured in final year of primary school (6th class) and first year of second-level school (1st year). In the sixth class, 261 participants (53% female, mean age 12.22 ± 0.48 years) were tested. In first year, 291 participants (48% female, mean age: 13.20 ± 0.39 years) were tested. In total, 220 participants were involved in the study at both timepoints. Cross-lagged regression in AMOS23, using full information maximum likelihood estimation, was conducted to test reciprocal and predictive pathways between variables. The full cross-lagged model showed acceptable fit (χ2 = 69.12, df = 8, p < 0.01, NFI = 0.93, CFI = 0.94). HRF was the strongest predictor of future PA (β = 0.353), and also predicted PC (β = 0.336) and MC (β = 0.163). Object-control MC predicted future PA (β = 0.192). Reciprocal relationships existed between object-control MC and PA, and between object-control MC and PC. HRF was the strongest predictor of PA. Object-control MC also predicted PA. PA promotion strategies should target the development of HRF and object-control MC in primary school to reduce the decline in PA frequently observed after the school transition.