Severe muscle weakness in Fanconi’s syndrome is rarely the result of mitochondrial cytopathy. We describe a rare case of a 9-year-old male with early onset of Fanconi’s syndrome. He developed severe proximal muscle weakness exacerbated by hypokalemia and hypophosphatemia in childhood. The muscle biopsy revealed increased accumulation of abnormal mitochondria and fat droplets in histochemical stains and electron microscopy. Mitochondrial cytopathy cannot be excluded in Fanconi’s syndrome with late onset of muscular impairment. Long-term follow-up of his clinical course is suggested to understand the natural history of this unusual case.