Asthma is more frequent and severe in individuals with obesity compared to those with normal weight. While inhomogeneity of lung ventilation due to distal airway obstruction is a key feature in asthma, the effect of obesity on ventilation homogeneity is unclear. We conducted a cross-sectional study comparing lung clearance index (LCI) using multiple breath nitrogen washout technique between children with normal weight and asthma (n = 97), overweight/obesity and asthma (n = 100), overweight/obesity and no asthma (n = 100), and children with normal weight and no asthma (n = 67). Spirometry, lung volumes, and fractional exhaled nitric oxide (FeNO) were obtained for comparison. Results showed no significant difference in LCI between overweight/obesity groups and normal weight groups and no significant correlation between LCI and body mass index (BMI). However, LCI was higher in the asthma groups compared to non-asthma groups (p = 0.017, p = 0.003). There was a significant negative correlation between LCI and FEV1% predicted, FEV1/FVC, and FEF25-75% predicted (r = -0.24, p < 0.001; r = -0.26, p < 0.001; r = -0.23, p < 0.001), and a positive correlation with RV/TLC (r = 0.17, p = 0.003) and FeNO (r = 0.29, p < 0.001). These findings indicate that obesity does not affect the homogeneity of lung ventilation. Therefore, alternative mechanisms should be considered to explain the association between asthma and obesity.