Clear cell carcinoma of the bladder is a rare, aggressive malignancy with fewer than 60 reported cases to date, and it has never been described in a pediatric patient. We describe a urinary bladder tumor in an 8-year-old girl, which demonstrated similar features to clear cell carcinoma of the female genital tract with additional strong expression of SV40 large T antigen by immunohistochemistry. The patient had a history of severe infantile Crohn’s disease refractory to medical therapy, necessitating eventual stem cell transplant, complicated by graft-versus-host disease. Subsequent magnetic resonance enterography showed an incidental mass arising from the bladder dome, for which a partial cystectomy was performed. Histologically, the tumor demonstrated high-grade cytologic features with hobnail morphology, organized in various architectures, including solid, papillary, and tubulocystic, with strong and diffuse expression of PAX8, CK7, p53, and SV40 by immunohistochemistry. Additional stains were performed, and SALL4, GATA3, and napsin A were focally positive, whereas ER, WT1, and p63 were all negative. The overall features were consistent with clear cell carcinoma. The patient is currently alive with no evidence of disease at 1-year follow-up, status post–partial cystectomy without adjunct therapy. Clear cell carcinoma of the bladder is a rare malignancy that may occur in pediatric patients and may be associated with polyomavirus.