Objective To summarize the best evidence of exercise intervention in children undergoing Hematopoietic Stem Cell Transplantation (HSCT), so as to provide a reference for implementing exercise intervention in this population. Methods Following the evidence "6S" pyramid model, the relevant literature on exercise in children undergoing HSCT was searched using computer in UpToDate, Cochrane Library, PubMed, CNKI and other databases. The search time interval was from the establishment of each database to February 19, 2023. Quality of included literature was evaluated by two researchers, and the evidence was extracted and summarized. Results A total of 12 articles were included: 3 guidelines, 1 clinical decision supports, 3 expert consensus reports, 3 systematic reviews and 2 randomized controlled trials. Finally, 25 pieces of best evidence from 7 aspects (exercise cognition, exercise benefits, exercise management, exercise evaluation, exercise principles, exercise prescription, exercise safety) were extracted. Conclusion The summarized best evidence on exercise intervention for children undergoing HSCT provides evidence for clinical practice. It is recommended that health professionals should fully consider the clinical situations to develop more detailed personalized exercise prescription.