Background B-Acute Lymphoblastic Leukemia can rarely present with extramedullary involvement to non-CNS/testicular sites. Extramedullary relapse of B-ALL after allogeneic hematopoietic stem cell transplant is not well described in the literature and has shown to demonstrate different clinical course than medullary relapse. Case presentation A 35-year-old female with a history of BCR-ABL negative B-ALL presented with recurrent extramedullary relapse of B-ALL with unusual leukemic infiltration to bone, female genital tract, gastrointestinal tract and peritoneum after having achieved remission with consolidative alloHSCT. She received multiple treatments but ultimately died of disease progression. The case also demonstrates aberrant pathologic and immunophenotypic findings. Conclusions Extramedullary relapse of ALL responds poorly to current standard treatments and is associated with dismal outcomes. This case stresses on the need for further studies to understand the risk factors and pathogenesis of extramedullary relapse to develop preventative and curative strategies.