Schizophrenia is a common psychiatric disorder with high heritability. The age of onset is an important phenotype of schizophrenia and may be under considerable genetic control. Our previous study showed that a single nucleotide polymorphism (SNP) rs139887 in sex-determining region Y-box 10 (SOX10) gene was associated with the age of onset in schizophrenia. The aim of this study was to evaluate the effect of another SNP rs139883 in the exon 4 of SOX10 on schizophrenia using an early-onset samples in the Han Chinese population. A total of 309 schizophrenic patients with onset before age 18 and 390 healthy controls were recruited for association study. No significant differences of allele or genotype frequencies were identified between the schizophrenic patients and controls. However, the C allele was significantly associated with an earlier age of onset in total patients and male patients (Kaplan-Meier log rank test P = 0.026; Kaplan-Meier log rank test P = 0.047, respectively), but not in females. In conclusion, the SOX10 rs139883 polymorphism influenced the age of onset of schizophrenia in a gender-specific manner and this may represent a vital genetic clue for the etiology of schizophrenia.