Autistic youth are more likely to experience traumatic events and may be more likely to develop trauma-related symptoms. However, accurately identifying trauma-related symptoms in autistic youth can be challenging. We examined post-traumatic stress disorder (PTSD) and other trauma-related diagnoses in youth with and without autism spectrum disorder (ASD) in a large, pediatric psychiatric emergency department (ED) in a diverse urban setting. Between March 2019 and November 2021, 2728 patients presented at our emergency psychiatric ED. Youth with ASD were 42% less likely to receive trauma-related diagnoses (prevalence ratio 0.58, 95% CI 0.41, 0.80) compared with youth without ASD. One possible explanation for this finding is that trauma-related symptoms are under-detected in youth with ASD during emergency psychiatric evaluations. There is a need for trauma screening and diagnostic instruments specifically tailored to the unique needs of youth with ASD to ensure optimal assessment and care.