Chromosomal translocations involving RUNX1 or ABL1 are frequently observed in haematologic neoplasms. Here, we describe a novel fusion between RUNX1 and ABL1 identified by mRNA sequencing in a recurrent case of B-cell acute lymphoblastic leukemia (B-ALL). Four in-frame transcripts were found, and the cells exhibited a BCR-ABL1+ ALL-like gene expression profile. The patient was a 12-year-old boy carrying a complex karyotype. He achieved complete remission (CR) after aggressive treatment with anti-CD19 chimeric antigen receptor modified T-cell (CD19 CAR-T) therapy followed by allogeneic hematopoietic stem cell transplant (HSCT). However, at 14 months after transplant, the patient developed bone marrow relapse. With sequential CD22 CAR-T and CD19 CAR-T infusions, he achieved minimal residual disease (MRD)-negative CR again and took olverembatinib and dasatinib as maintenance therapy. In summary, the novel fusions RUNX1::ABL1/ABL1::RUNX1 were identified for the first time in our patient, and truncated RUNX1 and ABL1 might play a pivotal role in relapse. These patients with ABL fusions may benefit from tyrosine kinase inhibitors (TKIs), but the function of RUNX1::ABL1 as well as ABL1::RUNX1 in vivo needs to be further investigated.