Background: Somatic mutations in WT1 and TET2 were separately perceived as contributors to hematopoietic disorders and thought to have a mutually exclusive effect in acute myeloid leukemia (AML). Here, we report a case in which WT1 and TET2 mutations co-existed at different stages in an AML patient with t(9;11)(p21.3;q23.3), and without abnormal WT1 expression, which did not synchronize with the patient's tumor state. Hence, the origins and prognostic value of these two mutations were investigated. Methods: Bone marrow (BM) and buccal mucosal cells were obtained from a 27-year-old male AML patient, and next-generation sequencing (NGS), targeting multiple genes, was performed after DNA extraction. Single nucleotide variant (SNV) and insertion-deletion (Indel) associated with AML were identified in these two samples by using SAM tools. Then, peripheral blood or buccal mucosal cells were obtained from the patient’s relatives, and NGS targeting multiple genes was applied. Besides, the relationship between overall survival (OS) and alteration of these two genes in AML patients was analyzed by using cBioPortal and UALCAN databases, respectively. Results: SNV of WT1 (NM_024426:exon7:c.1109G>C;p.Arg370Pro) and TET2 (NM_001127208:exon11:c.5530G>A;p.Asp1844Asn) were present in the BM of the patient, and these two mutations were also observed in his buccal mucosal cells, which suggested that they were germline mutations. Variation analysis of samples from other relatives indicated that WT1 (NM_024426:exon7:c.1109G>C;p.Arg370Pro) and TET2 (NM_001127208:exon11:c.5530G>A;p.Asp1844Asn) were also present in his father and mother, respectively. The patient’s brother also carried TET2 (NM_001127208:exon11:c.5530G>A;p.Asp1844Asn) mutations. Bioinformatic analysis suggested that mutations in the WT1 and TET2 genes are both associated with a poor prognosis of AML, and abnormal TET2 expression is associated with a poorer prognosis than abnormal WT1 expression. Conclusion: It is firstly report that WT1 p.Arg370Pro and TET2 p.Asp1844Asn mutations co-existed in an AML patient with t(9;11)(p21.3;q23.3) and no WT1 abnormal expression, which highlight the importance of the identification and prognostic evaluation of germline mutations in clinical practice for AML.