Background: Atypical cysts do not diagnostic criteria form classification as any of the variants of renal tumors, which have led to diagnostic difficulties. When these cysts have been encountered in surgical pathology practice it can be easily misdiagnosed as renal carcinoma and results in overtreatment. Case presentation: A 55-year-old Chinese woman with a right renal cystic mass came to our hospital. The computed tomography revealed bilateral cysts in both kidneys. In histology, the right renal cystic mass was arranged by stratified epithelium with short papillary projections and tufting. The covered epithelial cells were characterized by clear cytoplasm and small nuclei. Immunohistochemistry, these epithelial cells were diffusely positive for CK7, CK8, CK18, Vimentin and EMA, weakly positive for RCC and PAX-8, while diffusely negative for AMACR, CD10 and TFE-3. And the Ki-67 positive rate was 3%. Based on the immunohistochemical profile and histological features, the final diagnosis is an atypical renal cyst (clear cell type). The patient underwent right nephrectomy. The patient is alive and without any sign of subsequent renal cancer during 11 months of follow-up. Conclusion: Atypical renal cyst is extremely rare among the routine renal pathological diagnosis, we report this case to enhance the understanding and differential diagnosis of the atypical renal cyst and remind the pathologist of this precancerous lesion, and therefore, to avoid unnecessary or excessive treatment.