Physical activity (PA) is critical to improving health factors such as weight, adiposity, and aerobic fitness. However, children who meet PA guideline recommendations demonstrate developmental differences in health-related outcomes. To investigate prospective associations between PA behaviour (overall PA and PA intensity) and trajectories of health-related factors among physically active children. This prospective study (2.5 years) included 391 children (baseline age: 8.1 ± 1.4 years; girls 36.3%) from ten public schools. All children performed 60-min or more of moderate-to-vigorous physical activity (MVPA) per day objectively measured. Trajectories of BMI, waist circumference, and aerobic fitness were constructed with a group-based multi-trajectory model. Three trajectory subgroups were identified: 'high fitness/normal weight' (48.4% of children), 'moderate fitness /normal weight' (42.5% of children), and 'low fitness/overweight-obese' (9.1% of children). Children performing higher overall PA, were less likely of being classified as members of the 'Low Fitness/Overweight-Obese' [Relative Risk Ratio (RRR and 95% CI) = 0.56 (0.37 to 0.85) compared to 'high fitness/normal weight' subgroup. Each additional 5% in light PA time was associated with approximately twofold [RRR 2.12 (1.24-3.61)] increased risk of being in the 'low fitness/overweight-obese' trajectory relative to the 'high fitness/normal weight' trajectory. Each additional 2% in vigorous-PA time was associated with a 42% and 85% reduced risk (relative to 'high fitness/normal weight') of being in the 'moderate fitness/normal weight' [RRR 0.58 (0.38-0.96)] and 'low fitness/overweight-obesity' [RRR 0.15 (0.06-0.37)] trajectory, respectively. Overall PA and additional time in vigorous-PA was associated with improved health-related outcomes, while light PA was negatively associated with health-related outcomes among children who adhere to PA guideline recommendations. Vigorous PA was the strongest predictor of the health trajectories. All PA guidelines for children should place greater emphasis on the importance of vigorous PA.