Background: Treating severe childhood obesity has proven difficult with inconsistent treatment results. This study reports the results of the implementation of a childhood obesity chronic care treatment protocol.Methods: Patients aged 5 to 18 years with a body mass index (BMI) above the 99th percentile for sex and age were eligible for inclusion. At baseline patients' height, weight, and tanner stages were measured, as well as parents' socioeconomic status (SES) and family structure. Parental weight and height were self-reported. An individualised treatment plan including numerous advices was developed in collaboration with the patient and the family. Patients' height and weight were measured at subsequent visits. There were no exclusion criteria.Results: Three-hundred-thirteen (141 boys) were seen in the clinic in the period of February 2010 to March 2013. At inclusion, the median age of patients was 11.1 years and the median BMI standard deviation score (SDS) was 3.24 in boys and 2.85 in girls. After 1 year of treatment, the mean BMI SDS difference was -0.30 (95% CI: -0.39; -0.21, p < 0.0001) in boys and -0.19 (95% CI: -0.25; -0.13, p < 0.0001) in girls. After 2 years of treatment, the mean BMI SDS difference was -0.40 (95% CI: -0.56; -0.25, p < 0.0001) in boys and -0.24 (95% CI: -0.33; -0.15, p < 0.0001) in girls. During intervention 120 patients stopped treatment. Retention rates were 0.76 (95% CI: 0.71; 0.81) after one year and 0.57 (95% CI: 0.51; 0.63) after two years of treatment. Risk of dropout was independent of baseline characteristics. Median time spent by health care professionals was 4.5 hours per year per patient and the mean visit interval time was 2.7 months. The reductions in BMI SDS were dependent on gender, parental BMI, and family structure in girls, but independent of baseline BMI SDS, age, co-morbidity, SES, pubertal stage, place of referral, hours of treatment per year, and mean visit interval time.Conclusions: The systematic use of the TCOCT protocol reduced the degree of childhood obesity with acceptable retention rates with a modest time-investment by health professionals.