The recommended treatment for children with obesity includes numerous consultations by a multidisciplinary team, which is very cumbersome. Telehealth can assist in administering frequent care to children with obesity, yet the exact approaches and modes of delivery are still explored. During the COVID-19 pandemic, we developed an intensive telehealth-based treatment program that included a rewarding app for children with obesity. The aim of this study was to compare 6-month changes in body mass index (BMI) and body fat percent between participants in the program (n = 70) vs. children that underwent historic on-site care (n = 87). After 6 months, more participants in the telehealth group continued treatment compared to the on-site group (79% vs. 60%, p < 0.001). A significant reduction in the median BMI z-score (zBMI) was seen after 6 months in both groups (p < 0.01), with a similar proportion of zBMI reductions (71% in the telehealth group, 75% in the comparison group, p = 0.76). No statistically significant differences were found between the study groups in 6-month changes in BMI, zBMI, body fat percent or fat z-scores. We conclude that our telehealth program, which was executed during the COVID-19 pandemic, resulted in a high proportion of children with zBMI reduction that was comparable with the more personal on-site care.