Objective: To explore the feasibility of immunohistochemical markers in molecular classification of pediatric medulloblastoma and to analyze the correlation of protein expression with clinicopathological characteristics and prognosis. Methods: Elivision immunohistochemistry was used to detect the expression of β-catenin, Gli-1, NPR3 and KCNA1 protein in tissue microarray containing 40 paraffin embedded pediatric medulloblastoma specimens. Chi-square test and Fisher exact test was used to analyze the correlation of expression with gender, age, tumor location and pathological subtypes. Follow-up data was handled by using Kaplan-Meier survival analysis, Log-Rank test and Cox regression analysis. Results: Positive expression ratio of β-catenin, Gli-1, NPR3 and KCNA1 protein were 10%, 55%, 50% and 30%. The positive expression of Gli-1 was correlated with the age of the children and the pathological type (P>0.05). Kaplan-Meier survival analysis showed that the prognosis of patients with <3 years of age group and the Gli-1 positive group was poor (P<0.05). Cox proportional hazard regression analysis showed that the age, pathologic type, the expression of Gli-1 and NPR3 protein were independent prognostic factors in children with medulloblastoma (P<0.05). There were 4 cases of type WNT, 10 cases of type SHH, 6 cases of type 3, 2 cases of type 4. Kaplan-Meier survival analysis suggested that molecular subgroup was not associated with prognosis (P>0.05). Conclusion: Positive expression of β-catenin in nuclear or nuclear and cytoplasm can be used as a protein marker of WNT type. The expression of Gli-1 is closely related to the age of the children and the pathological types, the positive expression suggests that the prognosis was poor, and it was one of the independent prognostic factors in pediatric medulloblastoma. Accurate subgrouping needs to be combined with other molecular detection methods because there is partial overlap in expression of Gli-1 with NPR3 and KCNA1 protein.