The cost-effectiveness of childhood obesity prevention interventions is critical for their sustained implementation. This study evaluated the cost-effectiveness of the Educació en Alimentació (EdAl) program, a school-based intervention for reducing obesity. Total EdAl program implementation costs and per-child costs were estimated. Cost-effectiveness, defined using the incremental cost-effectiveness ratio (ICER), was estimated as the difference between the intervention and control group costs divided by the obesity-related outcome effects for boys (avoided cases of obesity, obesity prevalence, body mass index BMI, and BMI z-score units) for each group. As a significant difference (4.39%) in the reduction of obesity prevalence between the intervention and control groups was observed for boys in the EdAl program, the data were calculated only for boys. The intervention cost was 24,246.53 € for 1,550 children (15.64 €/child/3 years) or 5.21 €/child/year. The ICERs/boy were 968.66 € to avoid one case of obesity, 3.6 € to reduce the obesity prevalence by 1%, 44.68 € to decrease BMI by one unit, and 65.16 € to reduce the BMI z-score by one unit. The cost of reducing the obesity prevalence in boys by 4.39% was 5.21 €/child/year, half the cost proposed by the Spanish Health Ministry, indicating that the EdAl program is cost-effective.