The aim of the present study was to assess the prognostic value of circular RNA WW and C2 domain-containing protein 3 (circWWC3) in patients with clear cell renal cell carcinoma (ccRCC). The clinicopathological data were collected for patients with ccRCC treated between January 1, 2012, and February 31, 2014, at The Fourth Hospital of Hebei Medical University Hospital (Shijiazhuang, China). A total of 150 patients who underwent nephrectomy were included in the study. Analysis of stored tissues and long-term follow-up data was performed. Fluorescence in situ hybridization was used to detect the relative circWWC3 expression in fresh-frozen cancerous and adjacent para-cancerous tissue samples from patients with ccRCC. A χ 2 test was used to analyze the association between circWWC3 expression levels and the clinicopathological parameters of the patients. A Cox proportional risk regression model was used to analyze the clinical factors affecting patient prognosis. The survival curve was plotted using the Kaplan-Meier method, and the association between circWWC3 expression levels and patient survival status was tested using the log-rank test. circWWC3 expression in cancerous tissues was higher than that in the adjacent normal tissues. Additionally, circWWC3 expression was significantly associated with T stage (P= 0.005) and pathological grade (P= 0.033). Univariate Cox regression analysis showed that overall survival (OS) was associated with T stage, pathological Fuhrman grade and circWWC3 expression levels (all P<0.05). Multivariate Cox regression analysis also yielded similar results in patients with ccRCC (P<0.05). Moreover, the OS time of patients with high circWWC3 expression was significantly shorter than that of patients with low circWWC3 expression. In conclusion, high circWWC3 expression is an independent risk factor affecting patient prognosis, and is expected to be an important prognostic biomarker and novel therapeutic target for patients with ccRCC.