Objective Very few epidemiologic studies on bone fracture have been conducted in schools for handicapped children (Yogo schools). The aim of this study was to clarify the frequency and risk factors of bone fracture in physically disabled children in Japan. Methods We used a cross-sectional design to examine 525 physically disabled children in 38 Yogo schools in the Hokuriku-Koshinetsu District of Japan. The questionnaire surveyed information on participant sex, age, level of physical disability, and bone fracture history. Information on fractures was obtained, including number of fractures over participant lifetime, age when fractures occurred, location, and cause. One-year-period prevalence and lifetime prevalence were defined as the proportion of subjects with incident fractures in the previous year and with a history of fracture, respectively. Results Participant ages ranged from 6 to 15 years, and 66.3% had cerebral palsy (CP). The 1-year-period prevalence was 3.6% and lifetime fracture prevalence was 9.7%. The 1-year-period prevalence in the age groups of 6-9, 10-12, and 13-15 years was 2/184 (1.1%), 5/171 (2.9%), and 12/164 (7.3%), respectively (P for trend = 0.0031). There were no differences in period prevalence between sexes, and this was not associated with presence of CP. Multiple logistic regression analysis showed that age and presence of one joint contracture in the lower limbs or hip were independently associated with occurrence of bone fracture over participant lifetime. Conclusions Physically disabled children are at high risk of bone fracture, and further risk factors should be determined.