Pediatric anaplastic lymphoma kinase (ALK)-positive anaplastic large cell lymphoma (ALCL) usually has a benign clinical course. A small fraction of patients with ALCL develops an aggressive clinical course; however, its etiology remains unclear. Here we report on an ALK-positive ALCL patient, who had complex translocations with TPM3-ALK revealed by RNA sequencing, with a very aggressive clinical course. On admission, the patient had extraordinarily high white blood cell count with double ALK-translocated chromosomes, and subsequently developed a more aggressive transformation with invasion into multiple organs with triple ALK-translocated chromosomes. The aggressive clinical course may have been related to these additional chromosomal aberrations. Our report provides new insights into the clonal evolution in ALCL and suggests the importance of monitoring examinations including fluorescence in situ hybridization analysis.