Autistic youth bullied at school are at risk for school refusal (SR), which may grow from emerging SR (ESR). SR and ESR have been associated with social phobia and separation anxiety among neurotypical youth but these associations have not been studied among autistic youth. The associations between both types of anxiety and in a sample of 71 autistic boys aged 6 to 18 years (M = 10.23, SD = 1.43). Eighty-two percent of boys reported being bullied at school, and 55% of these boys asked to stay home from school. Boys who asked to stay home had a significantly higher level of separation anxiety than boys who did not ask to stay home. There was no difference between these two groups with respect to levels of social phobia. At the item level, two of the four social phobia symptoms were significantly correlated with the request to stay home from school as were seven of the eight symptoms of separation anxiety. Results suggest that autistic boys bullied at school do not seek to avoid school because they are shy in social situations, but because they want to spend time with their parents. Implications for intervention are discussed.