Objective To detect the expression of FAT1 gene in children with medulloblastoma and analyze the role of FAT1 gene in prognosis. Methods A total of 58 cases with medulloblastoma were collected from January 2004 to December 2016. The mutation in FAT1 gene was determined by whole exome sequencing (WES) and confirmed by Sanger sequencing. The expression of FAT1 in medulloblastoma tissues was determined by real-time fluorescent quantitative polymerase chain reaction (FQ-PCR) technology and immunohistochemistry assay. RNA interference (RNAi) technology was used to reduce FAT1 gene expression in tumor cells and cell viability was detected by MTS method. Kaplan-Meier analysis was used to draw survival curve. Log-Rank test was used to assess the association of FAT1 gene expression with overall survival (OS) and survival rate and clinical factors of different groups of expression. Results 1) WES indicated 7 missense mutations in 8 tissues including 187517703C > G, 187521337T > C, 187524503A > T, 187541859C > T, 187584610C > G, 187628338G > A, 187630615G > A, and the mutations were confirmed by Sanger sequencing. 2) By real-time FQ-PCR assay and immunohistochemistry, the expression of FAT1 in tumor tissues was significantly lower than in normal brain tissue (P=0.012). 3) The knockdown efficiency of two targets (shFAT1 and shFAT2) was over 70%. Cell proliferation rate was increased significantly after FAT1 gene knockdown (P<0.01). 4) Based on the expression of FAT1 by immunohistochemistry, 20 cases demonstrated high FAT1 expression (positive staining >50%) and 38 cases demonstrated low FAT1 expression (positive staining ≤ 50%). The OS and survival rate of patients with low FAT1 expression was significantly shorter than high FAT1 expression group (P=0.009, for all). 5) The ratio of patients less than 3-years old (P=0.037) and cystic change (P=0.002) in low FAT1 patients was higher than the control. But no difference was found in sex, tumor calcification and Chang's tumor classification. Conclusions Children with low FAT1 gene expression displayed worse prognosis. FAT1 gene expression could predict the prognosis of patient.