Animal studies have strongly implicated a role of S100B in spatial ability and our recent study of humans found that S100B gene polymorphisms (rs9722, rs1051169, and rs2839357) were associated with schizophrenia patients' spatial ability (as assessed by a block design task and a mental rotation task). In this study, we explored the associations between these and three additional SNPs in S100B and prefrontal functions (working memory and executive control) among 434 schizophrenia patients and 412 healthy controls. Results showed that, for both schizophrenia patients and healthy controls, two SNPs were significantly associated with prefrontal functions in the spatial domain (P value threshold was set at 0.014 after correcting for multiple comparisons), with the AA genotype of rs9722 and the GG genotype of rs2839357 linked to poorer performance. No SNP was associated with prefontal functions in the verbal domain (all Ps >0.05). These results extend our previous study and further confirm the important roles of the S100B gene in spatial abilities.