The combined role of objectively assessed moderate-vigorous intensity physical activity (MVPA) and sedentary behaviour (SB) is unclear in obesity prevention. This study aimed to identify latent groups for MVPA and SB trajectories from childhood to adolescence and examine their relationship with obesity risk at adolescence. From the Gateshead Millennium Study, accelerometer-based trajectories of time spent in MVPA and SB at ages 7, 9, 12, and 15 were derived as assigned as the predictor variable. Fat mass index (FMI), using bioelectrical impedance at age 15, was the outcome variable. From 672 children recruited, we identified three distinct multiple trajectory groups for time spent in MVPA and SB. The group with majority membership (54% of the cohort) had high MVPA and low SB at childhood, but MVPA declined and SB increased by age 15. One third of the cohort (31%) belonged to the trajectory with low MVPA and high time spent sedentary throughout. The third trajectory group (15% of the cohort) that had relatively high MVPA and relatively low SB throughout had lower FMI (−1.7, 95% CI (−3.4 to −1.0) kg/m2, p = 0.034) at age 15 compared to the inactive throughout group. High MVPA and low SB trajectories when combined are protective against obesity.