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Aim Glypican-3 (GPC3) is a membrane-associated heparan sulfate proteoglycan involved in regulation of cell proliferation, cell survival, cell migration and differentiation process. MicroRNAs (miRNAs) are single-stranded, non-coding functional RNAs that are important in many biological processes. GPC3 and miRNAs have been found to play essential roles in the development and progression of hepatocellular carcinoma (HCC). However, little information about the relationship between GPC3 and miRNAs is available nowadays. Therefore, this study aims to examine the relationship between GPC3 and miRNAs. Methods Dual-luciferase reporter assay was used to validate the direct target of GPC3. Fluorescence quantitative PCR and Western blotting were used to examined the gene expression at mRNA and protein levels. Cell apoptosis was evaluated by flow cytometric analysis and Annexin V-FITC staining. Invasion of cells was evaluated by Transwell matrigel assay. Results The results showed that miR-520c-3p could specifically target GPC3 in HCC cells. GPC3 protein levels decreased with unchanged transcription efficiency after miRNA transfection, and there was negative correlation of miR-520c-3p expression in HCC in relate to GPC3 protein levels. Moreover, miR-520c-3p not only induced HCC cell apoptosis, but also inhibited the growth and invasion of the cells. Interestingly, overexpression of GPC3 could effectively reverse apoptosis induced by miR-520c-3p transfection in HCC. Conclusions Taken together, these results supported that miR-520c-3p may decrease GPC3 protein levels to inhibit proliferation of HCC cells. Therefore, GPC3 could be a new target for genetic diagnosis and treatment of HCC.