Cystinuria, one of the first inborn errors of metabolism, is characterized by hyperexcretion of cystine, arginine, lysine, and ornithine into urine. Cystinuria is genetically classified into types A and B. Mutations in the SLC3A1 gene lead to type A, and type B is caused by mutations in the SLC7A9 gene. We described a 19-year-old woman that had early onset of cystine calculus formation at the age of 3 years. After DNA extraction and polymerase chain reaction, direct sequencing was performed. By these methods, a novel nucleotide substitution c.177G>A in exon 3 of the SLC7A9 gene was found, which had not been reported elsewhere previously. This nucleotide substitution occurs in the extracellular domain of the SLC7A9 gene. In addition, a previously described intron variant c.1136+2/3delT (intron 6 of SLC3A1) in homozygosity status was detected in the patient. To our knowledge, this is the first report of novel nucleotide substitution c.177G>A in exon 3 of the SLC7A9 gene.