Background: Novel fusion genes such as ZNF384 have been identified in B-cell precursor acute lymphoblastic leukemia (BCP-ALL) in recent years. Patients harboring ZNF384 rearrangement have a distinctive immunophenotype with weak CD10 and aberrant CD13 and/or CD33 expression, which makes ZNF384-rearranged ALL a unique subtype of BCP-ALL. However, research on the prognostic significance of ZNF384 rearrangement has been limited to date.Case presentation: We described a 17-year-old young woman who was diagnosed with ALL and had kidney involvement as the first manifestation, which was very rare in the existing studies. FISH analysis indicated a rearrangement of ZNF384 according to its probe. The patient had a typical characteristic immunophenotype of ZNF384 rearrangement with CD10 being negative but CD13 and CD33 being positive. She had an unfavorable prognosis since she responded poorly to chemotherapy and developed a relapse shortly after reaching CR.Conclusion: The importance of the ZNF384 gene rearrangement in terms of prognosis remains unclear. We reported a young woman harboring ZNF384 rearrangement in ALL with kidney involvement. She experienced different treatments, but her prognosis remained poor. Since ZNF384 rearrangement may act as a negative prognostic predictor, early detection based on its characteristic immunophenotype is of great necessity.