We present the case of a 15-year-old adolescent boy with recurrent precursor B-cell acute lymphoblastic leukemia, which appeared 9 years and 7 months after a first unrelated allogeneic hematopoietic stem cell transplantation (HSCT). The patient received chemotherapy and a subsequent second unrelated allogeneic HSCT, and was free of the disease 3 years after the second HSCT. A molecular study revealed the same rearrangement pattern at IGK@ in both the first relapse and the later relapse, confirming the common origin of the leukemic blasts at different time points. However, a new Vδ2-Dδ3 rearrangement of TRD@ emerged at the later relapse. A subsequent, more sensitive examination revealed a minor subpopulation with rearrangements at both IGK@ and TRD@, even during the first relapse. This finding suggests that the minor clone, related to the major clone, was present at the first relapse, leading to the later recurrence, even though the major clone at the first relapse had been eradicated by the first allogeneic HSCT. Although a later relapse after allogeneic HSCT is a rare phenomenon, clinicians should keep in mind that later relapses can occur, even after allogeneic HSCT.