Background As few longitudinal studies have examined how active transport is associated with physical activity among children and adolescents over time, and how active transport tracks through childhood and adolescence, it is important to understand whether physically active children retain their activity patterns through adolescence. This study aimed to examine (a) tracking of active transport and of moderate-to-vigorous physical activity (MVPA) across childhood and adolescence in two age cohorts; and (b) associations between active transport and MVPA at three distinct time-points, over five years. Methods This longitudinal study of two cohorts aged 5-6 years (n = 134) and 10-12 years (n = 201) at baseline (T1), in Melbourne, Australia, gathered follow-up data at three (T2) and five years (T3). Walking/cycling to local destinations was survey-reported; while MVPA was recorded using accelerometers and mean time spent daily in MVPA on week days and on weekends was computed. Tracking of these behaviours was examined over five years using General Estimating Equations. Linear regression analyses were performed to examine associations between active transport and MVPA at each time-point. Results Active transport tracked moderately among children (boys, βs = 0.36; girls, βs = 0.51) but not among adolescents. Physical activity tracked moderately (βs value range: 0.33-0.55) for both cohorts. Active transport was not associated with children's MVPA at any time-point, but was associated with adolescent boys' MVPA on week days at T1 (B = 1.37 (95% CI: 0.15, 2.59)), at T2 (B = 1.27 (95% CI: 0.03, 2.51)) and at T3 (B = 0.74 (95% CI: 0.01, 1.47)), and with adolescent girls' MVPA on week days (B = 0.40 (95% CI: 0.04, 0.76)) and on weekends (B = 0.54 (95% CI: 0.16, 0.93)) at T3 only. Conclusion Active transport was associated only with boys' MVPA during early adolescence and with boys' and girls' MVPA during late adolescence. While active transport should be encouraged among all school-aged children, it may provide an important source of habitual physical activity for adolescent girls, in particular, among whom low and declining physical activity levels have been reported world-wide.