Acute lymphoblastic leukemia (ALL) is the most common form of pediatric leukemia in Japan and presents significant treatment challenges owing to variable patient sensitivity to the key therapeutic agent, 6-mercaptopurine. This variability is often linked to genetic differences, particularly variants of NUDT15, which can lead to severe myelosuppression and an increased risk of second malignancies. Current methods for assessing NUDT15 variants must be improved for precise dosage adjustments. However, there is no reliable analytical method to determine the diplotype of NUDT15. Therefore, we aimed to develop a practical diplotyping method using digital PCR to enhance clinical outcomes and reduce complications. We performed a retrospective observational analysis of 38 pediatric ALL cases, employing digital PCR for NUDT15 genotyping and diplotyping. Nine patients had single NUDT15 variants, and two had multiple variants. We utilized digital PCR with four variant-specific probes and successfully detected compound heterozygosity in one patient who had multiple variants with variants in both exons 1 and 3. Collectively, our method enables detailed diplotype analysis and establishes digital PCR as a valuable tool for assessing NUDT15 variants. This approach has potential for tailoring treatment strategies for pediatric ALL and could substantially reduce treatment-related toxicity and enhance patient management outcomes.