The aim of this paper was to study the effect of long-term supervised exercise-induced weight maintenance on metabolic risk factors and physical fitness in obese children in early puberty. A total of 49 obese children aged 12–14 years were divided into control and exercise groups. The children in the exercise group accepted exercise intervention supervised by a professional sports teacher for 9 of the 12 months. All participants in both groups received health education once every 3 months. Anthropometry and fasting serum lipids, glucose, insulin and homeostatic model assessment for insulin resistance (HOMA-IR) were measured at months 0, 3, 9, 12 of the intervention. Physical fitness was determined before and after intervention. After the intervention (i) BMI was reduced by 0.6 (P < 0.05) in the exercise group, but increased by 0.5 (P < 0.05) in the control group, compared with the pre-intervention level at the end of 9-month intervention; (ii) Triglyceride levels in the exercise group significantly decreased by 23.1% by 3 months (P < 0.05), and by 30.2% after 9 months (P < 0.05), but increased by 50% (P < 0.05) in the control group; high density lipoprotein-cholesterol (HDL-C) decreased more by 35% (P < 0.05) in the controls than in the exercise group (P < 0.05); (iii) Fasting serum glucose, insulin level and HOMA-IR decreased, respectively, by 23.1%, 36.6% and 48.5% in the exercise group at 9 months (P < 0.05), whereas glucose levels increased by 10.9% (P < 0.05) in the control group; (iv) Exercise performance, such as upper- and lower-limb strength, flexibility and endurance, were enhanced by 17.9%, 12.3%, 22.3% and 20.4% (P < 0.01), respectively and (v) At 12 months, i.e. 3 months after terminating the supervised exercise, serum triglycerides, glucose, insulin and HOMA-IR level all returned to the pre-intervention level. Supervised decrement exercise can effectively slow the progress of obesity, improve insulin sensitivity and metabolic risk factors, but once the supervised exercise is stopped, the health benefits weaken or vanish. The key to helping these obese children is for them to cultivate good exercise habits which are sustained throughout their lives.