We report the case of a 5-year-old boy with mitochondrial cytopathy due to a partial deficiency of cytochrome c oxidase who had isolated proximal renal tubular acidosis and hypercalciuria. The patient developed hypotonia and blepharoptosis and exhibited growth retardation. Biochemical examination of muscle tissue revealed a partial deficiency of cytochrome c oxidase. He was treated with an alkali, hydrochlorothiazide, and indomethacin. After treatment, metabolic acidosis and hypercalciuria improved, and the patient had a catch-up growth phase. This case emphasizes the importance of performing renal tubular functional investigations and treatment in patients with mitochondrial cytopathy, even in the absence of multiple proximal tubular dysfunction.