Dysregulation of microRNAs (miRNAs) has been suggested to contribute to malignant progression of glioma. Previous studies have demonstrated that miR-539 is dysregulated in malignant progression of cancers. However, the potential role and mechanism of miR-539 in the progression of glioma remains unclear. In this study, we aimed to investigate the expression status and functional significance of miR-539 in glioma. We found that miR-539 expression was significantly decreased in glioma cell lines and tissues. Overexpression of miR-539 markedly inhibited glioma cell proliferation and invasion, while miR-539 suppression exhibited the opposite effect. Bioinformatics analysis and dual-luciferase reporter assays showed that miR-539 directly targeted the 3′-untranslated region of Disheveled-axin domain containing 1 (DIXDC1). DIXDC1 expression was negatively regualted by miR-539 overexpression. An inverse correlation between DIXDC1 mRNA expression and miR-539 expression was found in glioma specimens. Furthermore, knockdown of DIXC1 significantly inhibited proliferation, invasion and Wnt signaling in glioma cells. Overexpression of DIXDC1 partially reversed the inhibitory effect of miR-539 on glioma cell proliferation and invasion. Overall, these findings demonstrate that miR-539 inhibits glioma cell proliferation and invasion by targeting DIXDC1. Our study suggests that the miR-539 may serve as a potential target for the clinical diagnosis and treatment of glioma.