Abstract Background This study estimated the lifetime cost-effectiveness and equity impacts associated with two lifestyle interventions in the Dutch primary school setting (targeting 4–12 year olds). Methods The Healthy Primary School of the Future (HPSF; a healthy school lunch and structured physical activity) and the Physical Activity School (PAS; structured physical activity) were compared to the regular Dutch curriculum (N = 1676). An adolescence model, calculating weight development, and the RIVM Chronic Disease Model, calculating overweight-related chronic diseases, were linked to estimate the lifetime impact on chronic diseases, quality adjusted life years (QALYs), healthcare, and productivity costs. Cost-effectiveness was expressed as the additional costs/QALY gained and we used €20,000 as threshold. Scenario analyses accounted for alternative effect maintenance scenarios and equity analyses examined cost-effectiveness in different socioeconomic status (SES) groups. Results HPSF resulted in a lifetime costs of €773 (societal perspective) and a lifetime QALY gain of 0.039 per child versus control schools. HPSF led to lower costs and more QALYs as compared to PAS. From a societal perspective, HPSF had a cost/QALY gained of €19,734 versus control schools, 50% probability of being cost-effective, and beneficial equity impact (0.02 QALYs gained/child for low versus high SES). The cost-effectiveness threshold was surpassed when intervention effects decayed over time. Conclusions HPSF may be a cost-effective and equitable strategy for combatting the lifetime burden of unhealthy lifestyles. The win-win situation will, however, only be realised if the intervention effect is sustained into adulthood for all SES groups. Trial registration Clinicaltrials.gov (NCT02800616). Registered 15 June 2016 – Retrospectively registered.