Wnt-5a is a protein that is encoded by the WNT5A gene and is a ligand for the ROR2 receptor. However, its biological impact on clear cell renal cell carcinoma (ccRCC) remains unclear. In this study, the prognostic significance of concurrent WNT5A and ROR2 expression levels was observed to predict unfavorable overall survival and disease-specific survival. High Wnt-5a expression was detected in a ccRCC cell line panel but not in HK-2 cells, a normal proximal tubular cell line. Inhibition of DNA methyltransferase by 5-azaC in 786-O and Caki-2 cells resulted in Wnt-5a upregulation, indicating potential epigenetic modification. Furthermore, the results revealed the repression of cell movement in vitro and metastatic colonization in vivo upon WNT5A and ROR2 knockdown. The suppressions of angiogenesis in vivo and tubular-like structure formation in endothelial cells in vitro were also observed after silencing WNT5A and ROR2 expression. In addition, alteration in the downstream gene signature of the Wnt-5a-ROR2 signaling was discovered to be similar to that in MTA1-CTNNB1 axis. Moreover, prunetin treatment was found to reverse the gene signature derived from Wnt-5a-ROR2 signaling activation and to abolish ccRCC cell migration and proliferation. Overall, this study demonstrates the clinical and functional significance of the Wnt-5a-ROR2 axis and identify prunetin as a potential precision medicine for ccRCC patients harboring aberrant Wnt-5a-ROR2 signaling pathways.