Background: Many studies have examined sex differences in specific types of childhood disability, but data on the full range of disability are limited. Such data allow comparisons among disabilities and are valuable to the inference of etiology. To provide benefits and services, the Taiwanese government certifies disabled citizens and maintains a registry. We used the registry to evaluate sex differences in childhood disability and assess changes over time.Methods: We analyses the registry data from 2000 to 2011 and included all children who were at least 3 years of age, because certification before 3 years of age was discouraged by the government. We calculated the male-to-female rate ratios (RRs) for all disabilities combined and nine major disability categories, namely autism spectrum disorders (ASD), hearing impairment (HI), intellectual disability (ID), loss of function of major organs (LFMO), motor disability (MD), multiple disabilities, speech and language disability (SLD), visual impairment (VI), and other disabilities. In addition, we assessed the changes in the RRs over time.Results: The total number of cases between 3 to 17 years of age registered each year ranged between 49242 and 61717. Males generally had higher prevalence than females, and disabilities due to primarily neurodevelopmental conditions (ASD, ID, and SLD) had higher male-to-female RRs than disabilities due to primarily physical conditions (HI, LFMO, MD, and VI). The RRs of all disabilities combined increased over time, but the sex differences in ID, MD, and “other disabilities” decreased over time, while those in ASD, SLD, and multiple disabilities increased. The RRs of all disabilities combined decreased with age in most years, but the trends were different across individual disabilities.Conclusions: Male is the disadvantaged sex for childhood disabilities. The sex differences in disabilities due to primarily neurodevelopmental conditions were more prominent than those in disabilities due to primarily physical conditions. With the decreasing number of children given birth and growing awareness of sexual disparity during the study period in Taiwan, the RRs had an increasing time trend, instead of decreasing, which suggested that genetic causes have larger contributions to the sex differences in childhood disability than environmental causes.