Background <p>Bladder cancer poses a significant global health challenge, with a complex pathogenesis that includes a subpopulation of cancer stem cells (CSCs) contributing to therapy resistance and tumor recurrence. Identifying and understanding the role of CSC markers are crucial for developing targeted therapies and improving prognosis.</p> Objective <p>This systematic review and meta-analysis aimed to assess the clinicopathological significance and prognostic value of CSC markers in patients with bladder cancer.</p> Methods <p>A comprehensive literature search was performed according to PRISMA guidelines, identifying studies that evaluated CSC markers in bladder cancer. The methodological quality of included studies was assessed using the Newcastle-Ottawa Scale, and data were extracted for quantitative analysis.</p> Results <p>In total, 13 studies were included in the final analysis, covering a range of CSC markers including CD44, CD44v9, Nanog, Sox2, ALDH1, ALDH1A1, Sox4, Notch-1, and Oct-4. The expression of CD44, CD44v9, and ALDH1A1 was significantly associated with poor survival outcomes. The combined expression of CD44 and Nanog emerged as an independent prognostic factor for recurrence-free survival. Additionally, Sox2, Sox4, Notch-1, and Oct-4 were found to be correlated with tumor progression and aggressiveness.</p> Conclusions <p>Certain CSC markers, notably CD44, CD44v9, and ALDH1A1, are significantly associated with adverse survival outcomes in bladder cancer. These markers could serve as potential prognostic indicators and therapeutic targets. Further research is needed to elucidate the roles of Sox2, Sox4, Notch-1, and Oct-4 in bladder cancer prognosis.</p>