<b><i>Background: </i></b>Considering the large economic consequences of severe childhood obesity for the society, we aimed to conduct an economic evaluation comparing two intensive 1-year lifestyle treatments with varying inpatient periods for severely obese children and adolescents with regard to standard deviation score BMI (SDS-BMI) and quality-adjusted life years (QALYs). <b><i>Methods: </i></b>An economic evaluation from a societal perspective accompanying a randomized controlled trial with a 24-month follow-up. 80 participants (8-19 years) with severe obesity were included. Participants received an intensive 1-year lifestyle treatment with an inpatient period of 2 months (short-stay group) or 6 months (long-stay group). Data were collected at baseline, 6, 12 ,and 24 months and included SDS-BMI and QALYs. <b><i>Results: </i></b>SDS-BMI decreased in the first 6 months of treatment, stabilized in the second 6 months, and increased during the 2nd year in both groups. After 24 months, SDS-BMI was similar in both groups, but remained lower than baseline values (mean difference -0.24, 95% CI -0.42; -0.06). There was no difference in QALYs between the groups after 24 months. For SDS-BMI, the probability of the short-stay treatment being cost-effective in comparison with the long-stay treatment was 1 at a willingness-to-pay of 0 EUR/unit of effect, which slowly decreased to 0.54 for larger willingness-to-pay values. <b><i>Conclusions: </i></b>Based on the results of this study, the short-stay treatment is considered to be more cost-effective from the societal perspective in comparison with the long-stay treatment. Future research should provide insight in whether the short-stay treatment is cost-effective in comparison with usual care.