Substantial efforts have been dedicated to understanding, assessing, and managing suicide risk in youth broadly. However, little attention has been focused specifically on autistic youth and youth with intellectual disability. Because emergency departments are an essential point of suicide-related care, we used the National Emergency Department Sample databases to explore differences in prevalence of U.S. emergency department visits with a suicidal ideation or intentional self-inflicted injury ICD-9 diagnostic code by autistic youth, youth with intellectual disability, and youth without these diagnoses (i.e. the comparison group). Emergency department visits with a suicidal ideation or intentional self-inflicted injury diagnosis were more prevalent in autistic youth (5.1%) and youth with intellectual disability (6.6%) than in the comparison group (1.2%). Similar results were found when examining visits with a suicidal ideation diagnosis and with an intentional self-inflicted injury diagnosis separately. Prevalence of these emergency department visits increased more from 2006 to 2014 in autistic youth and in youth with intellectual disability than in the comparison group and were correlated with common and distinct sociodemographic and clinical factors across groups. Results suggest autistic youth and youth with intellectual disability may be uniquely vulnerable to suicide risk, highlighting the urgency of addressing suicidality and self-harm in these groups, particularly within emergency department settings.