Abstract. The involvement of the central nervous system (CNS) is rare in acute promyelocytic leukemia (APL). The present study reported the case of a 34-year-old male patient with APL that possessed a rare point mutation (p.Asn841Gly, c.2523C>A) in the tyrosine kinase domain of the FMS-like tyrosine kinase 3 (FLT3) gene and a novel Wilm tumor gene mutation (c.1209_1210insT/p.K404X). The patient suffered central nervous system and systemic relapses twice during systemic and intrathecal chemotherapy. At present, the patient is undergoing alternative induction and consolidation therapies, including the administration of FLT3 inhibitor, tetraarsenic tetrasulfide and novel cytotherapy, and is prepared for salvage allogeneic hematopoietic stem cell transplantion (allo-HSCT). The present study indicated that patients with APL that are at a high risk of relapse and unfavorable gene mutations should receive immediate allo-HSCT, whenever possible.