Cancer stem cells promote tumor progression, drug-resistance, and relapse, and many microRNAs (miRNAs) play critical roles in the expansion of cancer stem cells. In the present study, we investigated the role of miR-1301-3p in the expansion of prostate cancer stem cells; miR-1301-3p was significantly upregulated in prostate cancer cells and tissues compared with normal prostate cells and tissues. Sphere formation and side population assays suggested that miR-1301-3p promoted the expansion of prostate cancer stem cells, and increased the expression of prostate cancer stem cell-associated genes, such as OCT4, SOX2, NANOG, CD44, KLF4, c-MYC, and MMP2. MiR-1301-3p targeted Wnt pathway inhibitors, GSK3β and SFRP1, and inhibited their expression by directly binding to their 3′ untranslated regions. TOP/FOP luciferase assays suggested that miR-1301-3p activated the Wnt pathway, which was confirmed by increased β-catenin expression in the nucleus. Furthermore, the miR-1301-3p level correlated negatively with GSK3β and SFRP1 in prostate cancer tissues. In summary, we found that miR-1301-3p promoted the expansion of prostate cancer stem cells by inhibiting GSK3β and SFRP1, and activating the Wnt pathway.