t(6;11)(p21;q12)/TFEB gene fusion-associated renal cell carcinoma is a recently recognized renal cell carcinoma caused by the formation of Alpha-TFEB fusion genes. Herein, we have reported a rare case. A 20-year-old female patient presented with a mass measuring 4.1 cm × 3.3 cm in left kidney, and radical left nephrectomy was performed. Then the patient underwent unmarkable prognosis without recurrence or metastasis in the 18-month follow-up. Microscopic findings showed the tumor mainly composed of medium and large epithelioid cells with the structures of solid nesting and pseudopapillary. The tumor cells showed well-circumscribed, abundant eosinophilic cytoplasm and obvious small nucleoli. Furthermore, multifocal hemosiderin deposition and focal osseous metaplasia were observed. The tumor cells were positive for E-cadherin and focally positive for HMB45, Melan-A, AE1/AE3, Vimentin, RCC and CK19. FISH analysis for TFEB break-apart probe revealed a break-apart signal pattern meaning TFEB gene rearrangement. t(6;11)(p21;q12)/TFEB gene fusion-associated renal cell carcinoma is a rare tumor that mostly occurs in young adults with a beneficial prognosis. Diagnosis is usually performed according to the age of the patients, the pathologic morphology and immunophenotype. Positive TFEB expression in neoplastic cell nuclei can be regarded as sensitive and specific diagnostic event for this type of tumor. TFEB gene break-apart and rearrangement in FISH test is crucial to the diagnosis of the disease.