Objective To summarize the construction plan of the Shanghai Children Rare Diseases Registry Database, and to retrospectively analyze the demographic characteristics and disease spectrum of the patients included in the database. We aim to clarify the distribution characteristics of rare diseases in children, and to provide data support for the construction of a high-level research-based patient cohort and the systematic management of patients with rare disease. Methods Based on the disease catalog from National Rare Diseases Registry System, we build a regional rare disease registration database that can connect to the hospital information system. Descriptive studies were conducted to analyze patient data in the database. Results A total of 6341 cases of rare disease patients diagnosed from 2008 to 2021 were included in the database, covering 109 kinds of diseases. The proportion of outpatients and inpatients was 59.4% (3764 cases) and 40.6% (2577 cases), respectively. The male to female ratio was 1.36∶1. Langerhans cell histiocytosis (11.3%), familial dilated cardiomyopathy (7.9%), hemophilia (5.5%), and neurofibroma (5.4%) accounted for the most cases. With the wide application of high-throughput sequencing technology, the number of pediatric rare disease patients with definite diagnosis has increased year by year, and more than 80% of children can get a clear diagnosis before the ten-year old. Conclusions The present study established a rare disease registry database that includes both outpatients and inpatients. We have described the disease spectrum and demographic characteristics of children with rare diseases, and also reflected the progress in the field of diagnosis of children’s rare diseases in recent years. This study will provide basic data support for further inclusion of more rare diseases and building a higher level database of children's rare diseases in multiple centers.