Anemia is known to be a significant public health problem in many countries. Most of the available information is incomplete or limited to special groups such as people with intellectual disability. The present study aims to provide the information of anemia prevalence and associated risk factors of children and adolescents with intellectual disability in Taiwan. We analyzed physical examination charts of 937 children and adolescents with intellectual disability at the age of 6–18 years from three special schools. We collected information on their demographic characteristics (age and gender), disability condition (type and level), BMI (weight and height) and measured blood hemoglobin concentration (Hb). There were 11.6% of children and adolescents with intellectual disability with anemia (boy <13 g/dl, girl <12 g/dl), and the factors of gender, age, disability level and BMI are significantly correlated to anemia in bivariant analyses in the study. In the logistic regression analysis, the model revealed that the factors of gender (OR = 0.63, 95% CI = 0.41–0.95), and age (OR = 3.21, 95% CI = 1.77–5.82) were variables that could significantly predict the anemia occurrence of the participants. The study highlights the anemia prevalence in children and adolescents with ID is a mild public health problem among people with intellectual disabilities, but to prevent the problems become worst; the health authority should include providing children and adolescents with adequate nutrition and appropriate health protections during early childhood.