Aim <p>Children with obesity are at greater risk of impaired well-being, yet limited knowledge exists regarding the long-term effects of lifestyle interventions on students’ well-being and learning-related functioning in school. This study examines the long-term impact of a 1-year and 3-year family-centered lifestyle intervention on school-related well-being and functioning in children living with obesity.</p> Subject and methods <p>This observational study included 319 children aged 5 to 10&#xa0;years with obesity (body mas index [BMI] ≥ 30&#xa0;kg/m², adjusted for age and sex) who participated in either a 1-year (<i>n</i> = 107) or 3-year intervention (<i>n</i> = 66) or no intervention (<i>n</i> = 146). The mean follow-up period was 23.7 ± 4.2&#xa0;months. School-related well-being and functioning were assessed using the Danish National Well-being Questionnaire and analyzed using multivariable logistic regression.</p> Results <p>The 3-year intervention group showed a significant decrease in loneliness (adjusted odds ratio [aOR] 2.02; confidence interval [CI] 1.00, 4.13) and bullying (aOR 2.75; CI 1.31, 5.77) compared to the 1-year intervention group. However, it did not show significant long-term effects compared to the non-intervention group. Conversely, the 1-year intervention group showed increased loneliness (aOR 0.55; CI 0.31, 0.97) and bullying (aOR 0.43; CI 0.24, 0.76) compared to the non-intervention group.</p> Conclusion <p>The longer 3-year lifestyle intervention was more effective than the 1-year intervention in improving long-term school-related well-being and functioning in children living with obesity.</p> Clinical trial registration <p>ClinicalTrials.gov identifier: NCT06555380 (registered August 12, 2024).</p>