BACKGROUND: The current study set out to elucidate the specific role of microRNA (miR)-206 in cholangiocarcinoma (CCA) cell biological activities by negatively modulating jumonji AT-rich interactive domain 2 (JARID2). METHODS: Firstly, human intrahepatic biliary epithelial cells and CCA cell lines were selected via the analysis of miR-206 and JARID2 expression patterns in CCA by qRT-PCR. Next, the target relation between miR-206 and JARID2 was predicted by Targetscan and validated using dual-luciferase reporter gene assay and RNA immunoprecipitation (RIP) assay. Subsequently, CCK-8 method, colony formation assay, scratch test, Transwell assay, and western blot analysis were performed to evaluate cancer cell development after the overexpression of miR-206 and/or JARID2, with levels of invasion-related proteins assessed. In addition, xenograft transplantation was also employed to confirm the role of miR-206 in vivo. Lastly, Ki-67 expression pattern was also quantified with immunohistochemistry. RESULTS: It was found that miR-206 was poorly expressed and JARID2 was highly expressed in CCA cell lines. Also, miR-206 overexpression brought about a suppressive effect on cancer cell proliferation, migration, and invasion. Furthermore, miR-206 was observed to target JARID2. Meanwhile, JARID2 overexpression promoted cell growth, while simultaneous overexpression of miR-206 and JARID2 impeded malignant cancer progression, indicating that miR-206 overexpression inhibited cell progression via targeting JARID2. Finally, in vivo experimentation illustrated that miR-206 overexpression suppressed tumor growth and weight, and inhibited the expressions of JARID2 N-cadherin, vimentin, and Ki-67. CONCLUSION: Altogether, our findings clarified that miR-206 inhibited CCA malignancy by negatively regulating JARID2.