This mixed methods study aimed to examine plausible body mass index (BMI) trajectories after exposure to a primary school-based lifestyle intervention to aid in estimating the long-term intervention benefits. BMI trajectories for children at control schools (mean 7.6 years of age) were modelled until 20 years of age through extrapolating trial evidence (N = 1647). A reference scenario assumed that the observed 2-year effects of the 'Healthy Primary Schools of the Future' (HPSF) and 'Physical Activity Schools' (PAS) were fully maintained over time. This was modelled by applying the observed 2-year BMI effects until 20 years of age. Expert opinions on likely trends in effect maintenance after the 2-year intervention period were elicited qualitatively and quantitatively, and were used for developing alternative scenarios. Expert elicitation revealed three scenarios: (a) a constant exposure-effect and an uncontrolled environment with effect decay scenario, (b) a household multiplier and an uncontrolled environment with effect decay scenario, and (c) a household multiplier and maintainer scenario. The relative effect of HPSF at 20 years of age was -0.21 kg/m2 under the reference scenario, and varied from -0.04 kg/m2(a) to -0.06 kg/m2(b), and -0.50 kg/m2(c). For PAS, the relative effect was -0.17 kg/m2 under the reference scenario, and varied from -0.04 kg/m2(a, b), to -0.21 kg/m2(c). The mixed methods approach proved to be useful in modelling plausible BMI trajectories and specifying uncertainty on effect maintenance. Further observations until adulthood could reduce the uncertainty around future benefits. This trial was retrospectively registered at Clinicaltrials.gov (NCT02800616).