Objective To understand the clinical characteristics, diagnosis and treatment methods and prognostic factors of extrapulmonary tuberculosis in children, so as to improve the level of diagnosis and treatment of this disease. Methods The clinical data of children with confirmed and clinically diagnosed extrapulmonary tuberculosis admitted to Beijing Children's Hospital from January 2011 to December 2020 were retrospectively analyzed. Results A total of 473 children with extrapulmonary tuberculosis were hospitalized, accounting for 36.3% (473/1303) of the children with tuberculosis, including 269 boys (56.9%) and 378 rural patients (79.9%). The median age of onset was 4.1 (1.2-9.9) years, and 250 patients (52.9%) were less than 5 years old. One hundred and ten children (23.3%) were confirmed by etiology or pathology, and 363 children (76.7%) were clinically diagnosed, of whom tuberculous meningitis was the commonest (202 cases, 42.7%). In 307 children's extrapulmonary samples, the positive rates of acid-fast staining smear, Xpert MTB/RIF, Mycobacterium tuberculosis culture and pathological examination were significantly different (P<0.01), and the positive rates of pathological examination and Xpert MTB/RIF were higher. Chest imaging of 313 patients indicated active or old tuberculosis. As of June 18, 2022, a total of 336 children were followed up, of whom 211 had a good prognosis and 125 had a poor prognosis (including 23 deaths). Multivariate logistic regression analysis showed that age≤5 years old was an independent risk factor for prognosis (P<0.05), and abdominal tuberculosis, bone and joint tuberculosis (with tuberculous meningitis as reference) were independent protective factors for prognosis (P<0.05). Conclusions About one-third of hospitalized children with tuberculosis have extrapulmonary tuberculosis, and tuberculous meningitis is the commonest. Most of the patients were clinically diagnosed, and the molecular diagnostic technique of Xpert MTB/RIF was highly sensitive to extrapulmonary tuberculosis specimens. The prognosis of children under 5 years old and tuberculous meningitis is relatively poor.