O-linked mannose β-1,2-N-acetylglucosaminyltransferase 1 (PomGnT1) constitutes one third of the O-linked glycoproteins in brain tissue. However, its functions have been seldom investigated in brain cancers. In this study, immunohistochemistry was used for the detection of the PomGnT1 protein in 133 cases of glioma tissues. Spearman correlation analysis was used for the relationship between PomGnT1 staining and the glioma grade. Receiver operating characteristic curve was used to measure the diagnostic value of PomGnT1 protein in the degree of glioma malignance. We found that PomGnT1 expression was correlated with glioma grade, and it could be used as a marker to distinguish low- and high-grade gliomas. Stably transfected U87 cells were constructed to overexpress short hairpin RNA of PomGnT1. Immunofluorescence test detected that this protein also could restrain the generation of U87 cells’ pseudopodia. Western blotting further showed that the PomGnT1 protein had an impact on the c-myc protein level. In conclusion, our data suggest that PomGnT1 protein was correlated with the malignance of glioma progression, the mechanism involved in glioma cell’s pseudopodium formation, and the expression of c-myc protein.