The aim of this randomized, placebo-controlled study was to explore the effect of metformin in children with a neurogenic or myogenic motor deficit, who are therefore prone to develop overweight, adiposity, and insulin resistance. Study participants (n = 42) had a mean age of 15.5 yr, a short stature (height -2.4 SD), a relatively high BMI (+1.7 SD), and a high body fat fraction (41.9% or +2.8 SD). Abdominal CT confirmed the high fat mass and disclosed a high fraction of visceral fat. As expected, insulin resistance was increased. As compared to placebo, metformin intake for 6 months exerted an insulin sensitizing effect and lowered weight (mean difference of 2 kg within 6 months, p = 0.007) and BMI (p = 0.016). Weight loss appeared to be primarily due to loss of visceral fat ( approximately 20% vs. placebo; p < 0.0001). Results were similar across diagnostic subgroups. In conclusion, metformin treatment for 6 months was associated with a rise in insulin sensitivity and with a reduction of visceral adiposity in children and adolescents with a primary muscle disorder or with a neural tube defect. These findings suggest that insulin resistance underpins, at least partly, the overweight and visceral adiposity of these patients, who are not necessarily obese.