Objective: To analyze the diagnosis and treatment of children with rare diseases in the pediatric intensive care unit (PICU), the distribution of disease types and populations, clinical characteristics, and the use of orphan drugs. Methods: A retrospective case summary was conducted. Data were collected from 105 children aged 29 days to <18 years with a confirmed diagnosis of rare diseases according to the "First Batch of Rare Disease Catalogue in China" who were admitted to the PICU of Beijing Children's Hospital, Capital Medical University from January 2020 to December 2022. Data including general information, auxiliary examinations, and treatment details for each patient were collected from the hospital's electronic medical record system. Patients were divided into age groups: infancy (29 days to<1 year), early childhood (1 to <3 years), preschool age (3 to<7 years), school age (7 to<13 years), and adolescence (13 to<18 years). The chi-square test was used to compare gender distribution differences among various rare diseases. Results: A total of 105 patients with 130 cases meeting the diagnostic criteria were included, accounting for 4.7% (130/2 754) of the total admissions to the PICU. The age at PICU admission was 5.3 (0.8, 9.5) years and there were 81 cases in male. The 3 most common types of diseases were endocrine, nutritional, and metabolic diseases (37 cases); followed by neurological disorders(32 cases); and congenital malformations, deformities, and chromosomal abnormalities(17 cases). The 5 most common rare diseases were methylmalonic acidemia (14 cases), mitochondrial encephalomyopathy (14 cases), atypical hemolytic uremic syndrome (12 cases), autoimmune encephalitis (12 cases), and idiopathic cardiomyopathy (9 cases). The distributions of common rare diseases varied among different age groups. In infants, atypical hemolytic uremic syndrome was most common (6 children). There was no statistically significant difference regarding gender among children with mitochondrial encephalomyopathy (13.6% (11/81) vs. 6.1% (3/49), χ2=1.77, P=0.184). Respiratory failure (36 cases) was the primary reason for rare diseases children to be admitted to the PICU. A total of 95 cases underwent mechanical ventilation, 39 cases received multidisciplinary collaborative diagnosis and treatment, and only 6 children received orphan drug therapy during their stay in the PICU. Conclusions: Rare diseases are not uncommon in PICU. Endocrine, nutritional and metabolic disorders, neurological disorders, congenital malformations, deformities, and chromosomal abnormalities were common. Methylmalonic acidemia, mitochondrial encephalomyopathy, atypical hemolytic uremic syndrome and autoimmune encephalitis have higher cases. Many children with rare diseases in the PICU have complex conditions those are challenging to treat, requiring multidisciplinary collaboration. The utilization rate of orphan drugs among children with rare diseases in PICU needs to be improved.