Urological cancer refers to cancer in organs of the urinary system and the male reproductive system. It mainly includes prostate cancer, bladder cancer, renal cancer, etc., seriously threatening patients’ survival. Although there are many advances in the treatment of urological cancer, approved targeted therapies often result in tumor recurrence and therapy failure. An increasing amount of evidence indicated that cancer stem cells (CSCs) with tumor-initiating ability were the source of treatment failure in urological cancer. The development of CSCstargeted strategy can provide a possibility for the complete elimination of urological cancer. This review is based on a search of PubMed, Google scholar and NIH database (http://ClinicalTrials.gov/) for English language articles containing the terms: “biomarkers”, “cancer stem cells”, “targeting/targeted therapy”, “prostate cancer”, bladder cancer” and “kidney cancer”. We summarized the biomarkers and stem cell features of the prostate, bladder and renal CSCs, outlined the targeted strategies for urological CSCs from signaling pathways, cytokines, angiogenesis, surface markers, elimination therapy, differentiation therapy, immunotherapy, microRNA, nanomedicine, etc., and highlighted the prospects and future challenges in this research field.