Abstract A uniform approach for costing school-based lifestyle interventions is currently lacking. The objective of this study was to develop a template for costing primary school-based lifestyle interventions and apply this to the costing of the “Healthy Primary School of the Future” (HPSF) and the “Physical Activity School” (PAS), which aim to improve physical activity and dietary behaviors. Cost-effectiveness studies were reviewed to identify the cost items. Societal costs were reflected by summing up the education, household and leisure, labor and social security, and health perspectives. Cost inputs for HPSF and PAS were obtained for the first year after implementation. In a scenario analysis, the costs were explored for a hypothetical steady state. From a societal perspective, the per child costs were €2.7/$3.3 (HPSF) and €− 0.3/$− 0.4 (PAS) per day during the first year after implementation, and €1.0/$1.2 and €− 1.3/$− 1.6 in a steady state, respectively (2016 prices). The highest costs were incurred by the education perspective (first year: €8.7/$10.6 (HPSF) and €4.0/$4.9 (PAS); steady state: €6.1/$7.4 (HPSF) and €2.1/$2.6 (PAS)), whereas most of the cost offsets were received by the household and leisure perspective (first year: €− 6.0/$− 7.3 (HPSF) and €− 4.4/$− 5.4 (PAS); steady state: €− 5.0/$− 6.1 (HPSF) and €− 3.4/$− 4.1 (PAS)). The template proved helpful for costing HPSF and PAS from various stakeholder perspectives. The costs for the education sector were fully (PAS) and almost fully (HPSF) compensated by the savings within the household sector. Whether the additional costs of HPSF over PAS represent value for money will depend on their relative effectiveness.