The study aimed to investigate the role of miR-124-3p and its potential molecular mechanism in papillary thyroid cancer (PTC). The expression of miR-124-3p and mitogen-activated protein kinase 4 (MAP2K4) in human thyroid follicular epithelial cell line (NTHY-ORI3-1) and human papillary thyroid carcinoma cell lines (SW1736, BCPAP, TPC-1 and K1) was measured by RT-qPCR. Cell proliferation was measured by CCK-8, while cell cycle and apoptosis rate were measured by flow cytometry. Invasive ability and migrative ability were measured by transwell assay and wound healing assay, respectively. Western blot was used to detect the levels of relative proteins. In vivo, TPC-1 cells transfected with miR-124-3p mimic were subcutaneously injected into the flank of the mice to form tumour. After successful modelling, mice were divided into two groups (n = 10): Control group and miR-124-3p mimic group. The present study showed that miR-124-3p was lowly expressed, while MAP2K4 was highly expressed in PTC cell lines. Besides, miR-124-3p targeted MAP2K4 and negatively regulated MAP2K4 in TPC-1 cells. In addition, miR-124-3p inhibited the proliferation and motility, and induced apoptosis and cell cycle arrest of TPC-1 cells by inactivating MAP2K4/JNK/JunD pathway. Furthermore, miR-124-3p inhibited tumour formation by downregulating MAP2K4 level in vivo. In conclusion, the study provided a novel molecular mechanism of miR-124-3p in the progress of PTC. SIGNIFICANCE OF THE STUDY: Papillary thyroid cancer (PTC) is the most important pathological type of thyroid cancer, accounting for 80% of thyroid cancer. miR-124-3p exhibited significant inhibitory role in the transformation and development of malignant tumours. However, in PTC, the roles and its potential molecular mechanism are unclear. Here, the study investigated the roles of miR-124-3p in the progress of PTC and its potential molecular mechanism. We found that miR-124-3p inhibited the proliferation and motility, and induced apoptosis and cell cycle arrest in PTC cells. This study provided a novel molecular mechanism of miR-124-3p in the progress of PTC.