Background Neuroblastoma (NB) is a malignancy of neural crest cells that typically occurs in children. Single nucleotide polymorphisms (SNPs) in the fat mass and obesity associated ( FTO) gene, a well-conserved gene, are related to tumorigenesis. However, there is a lack of evidence regarding the relationship between FTO gene SNPs and NB susceptibility. Methods TaqMan assay was performed to determine associations between FTO gene SNPs and the risk of NB in 898 patients and 1734 controls from eight medical centers in China. And stratification analysis was performed to assess the association between the selected FTO SNPs and NB susceptibility among different subgroups. Results There was no significant association between the selected FTO polymorphisms and risk of NB in both single locus analysis and combined analysis. Conclusion Our study shows that individuals with retroperitoneal NB and those with III+IV NB are more likely to present with FTO SNPs than other patients. Furthermore, participants with FTO rs8047395 GG genotype were more likely to develop III+IV stage NB than other participants.