MicroRNAs have been reported to play a crucial role in ovarian cancer (OC) as the most lethal malignancy of the women. Here, we found miR-506-3p was significantly down-regulated in OC tissues compared with corresponding adjacent nontumor tissues. Ectopic miR-506-3p expression inhibited OC cell growth and proliferation using MTT and colony formation assay. Additionally, flow cytometry analysis showed that the overexpression of miR-506-3p induced cell cycle G0/G1 phase arrest and cell apoptosis in OC cells. A luciferase reporter assay confirmed that the myotubularin-related protein 6 (MTMR6) was the target of miR-506-3p. The expression of MTMR6 was increased in OC tissues compared with adjacent tissues using immunohistochemistry. Elevated MTMR6 protein levels were confirmed in OC cells lines compared with immortalized fallopian tube epithelial cell line FTE187 using western blotting. In addition, knockdown of MTMR6 imitated the effects of miR-506-3p on cell proliferation, cell cycle progression and apoptosis in OC cells. Furthermore, rescue experiments using MTMR6 overexpression further verified that MTMR6 was a functional target of miR-506-3p. Our data indicate that miR-506-3p might serve as a tumor suppressor gene and propose a new regulatory mechanism of MTMR6 by miR-506-3p in OC.