Prostate cancer (PCa) and breast cancer (BC) present formidable challenges in global cancer-related mortality, necessitating effective management strategies. The present study explores non-canonical Wnt signaling in PCa and BC, aiming to identify biomarkers and assess their clinical and therapeutic implications. Co-expression analyses reveal distinct gene patterns, with five overlapping genes (SULF1, ALG3, IL16, PLXNA2 and RASGFR2) exhibiting divergent expression in both cancers. Clinical relevance investigations demonstrate correlations with TNM stages and biochemical recurrence. Drug correlation analyses unveil potential therapeutic avenues, indicating that Wnt5a and ROR2 expressions are related to MEK inhibitor sensitivity in cancers. Meanwhile, further correlation analyses were conducted between drugs and the other novel non-canonical WNT genes (ALG3, IL16, SULF1, PLXNA2, and RASGRF2). Our findings contribute to understanding non-canonical Wnt signaling, offering insights into cancer progression and potential personalized treatment approaches.