There is uniformed definition of rare diseases in children, which can be viewed as rare diseases that develop in childhood, or the childhood of patients with rare diseases. Rare diseases are rarely seen in clinical setting, various in types and difficult to diagnose and treat. In the past few years, with the rapid development of medical technology and the establishment and wide application of rare disease management systems, great progress has been made in the diagnosis and treatment of rare diseases. Although the management of rare diseases is being gradually expanded and enhanced, there are still challenges, or opportunities for further improvement. China is a vast country with imbalanced distribution of medical resources. In many places, people have limited knowledge about the pathogenesis of many rare diseases. Capacities vary in the detection, diagnosis, and treatment of rare disease in different places. As a result, most rare diseases are either misdiagnosed or not diagnosed at all. Therefore, it is of great significance to establish a hierarchical system for the management of rare diseases, i.e., appropriate triage, risk stratification, early diagnosis and scientific treatment, and integrate regional resources into rare disease management. Studies have confirmed the existance of heterogeneity of rare diseases, with more than half of them occurring at birth or in childhood and that they are associated with a high mortality rate and a high incidence of functional disabilities in survivors. Therefore, rare diseases in child-ren deserve more attention. Standardized, protocol-based, law-based management of rare diseases in children is in urgent need. The article aims to discuss the status quo of the management of rare diseases in children, to summarize the clinical progress of rare diseases in children and to explore its prospects in the future, in the hope to provide some reference for the management of rare diseases in children.