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Background: Pyruvate kinase deficiency (PKD) is an autosomal recessive disorder caused by a PK‐LR gene mutation. Allogeneic hematopoietic cell transplantation (HCT) is an effective cure for PKD. However, the experience of applying HCT in PKD is limited. Methods: We present a child with novel PK‐LR gene mutations who was successfully cured by matched unrelated donor peripheral blood stem cell transplantation (MUD‐PBSCT). Results: A 4‐year‐old, male patient suffered severe hemolytic anemia and jaundice 5 h after birth. Gene sequencing showed that the pyruvate kinase‐liver and RBC (PK‐LR) gene had a nonsense mutation in exon 5: c.602G>A (p.W201X), and large deletions in exons 3–9. Both of them were novel pathogenic mutations of the PK‐LR gene. After transplantation, the hemoglobin level became normal and the nonsense mutation was undetectable. Grade Ⅳ acute graft‐versus‐host disease (aGVHD) and extensive chronic graft‐versus‐host disease (cGVHD) occurred in the patient. However, the GVHD was controlled effectively. The patient is alive and has good quality of life 22 months post‐transplant, but has mild oral lichen planus‐like lesion. Conclusion: Gene sequencing contributes to the diagnosis of PKD. HCT is an effective method for curing PKD, but we should explore how to reduce severe GVHD. [ABSTRACT FROM AUTHOR]