Fanconi syndrome is a generalized functional disorder of the proximal tubule of the kidney and is characterized by aminoaciduria, glycosuria, hyperphosphaturia, dehydration, rickets, and growth failure. Nephrocalcinosis and hypercalciuria are rare manifestations of Fanconi syndrome. There is no case report of Fanconi syndrome complicated with nephrocalcinosis and hypercalciuria in Korea. A 6-year-old boy presented with genu valgum and waddling gaits for about 3 years. There was no family history of renal disease and his physical examination was normal except for genu valgum and corrected cleft lip and palate. Laboratory investigations showed generalized aminoaciduria, glycosuria, hyperphosphaturia, hypercalciuria, and low-molecular weight proteinuria including ${eta}$-microglobulin. Serum 25-OH vitamin $D_3$ was within the normal range, and $1,25-(OH)_2$ vitamin $D_3$ was elevated. Bilateral renal medullary hyperechogenicity was demonstrated by ultrasonography. Analysis of the CLCN5 gene revealed no mutation. Here we describe a boy with Fanconi syndrome complicated with nophrocalcinosis and discuss the differential diagnosis.