Insomnia subtypes have not been characterized in severely affected youth with autism spectrum disorder. We examined indices of clinical impairment (i.e. length of hospital stay, autism severity, nonverbal intelligence quotient, and adaptive and maladaptive behaviors) across insomnia subtypes in 427 psychiatrically hospitalized children with autism spectrum disorder (mean age = 12.8 ± 3.4; 81.3% male). Multivariate analysis with Bonferroni adjustment tested for differences in clinical impairment across insomnia subtypes adjusting for age and sex. Per parent report, 60% (n = 257) of children had at least one form of insomnia. The distribution of subtypes was sleep onset (26.1%, n = 67), sleep maintenance (24.9%, n = 64), early morning waking (4.3%, n = 11), and combined (44.7%, n = 115). There was a significant multivariate effect of insomnia subtypes on clinical impairment (Pillai’s Trace = 0.25, F = 2.78, p < 0.001). Sleep maintenance and early morning waking were associated with longer hospital stays. Early morning waking was also associated with greater autism symptom severity. In general, children with sleep-maintenance or combined insomnias scored lower on adaptive behaviors and higher on maladaptive behaviors. Sleep-maintenance and combined insomnias appear to be more indicative of or consequential for impaired behavioral functioning. Lay abstract Insomnia subtypes are not well understood in the most severely affected children with autism spectrum disorder. We examined length of hospital stay, autism severity, nonverbal intelligence quotient, and behavioral functioning across insomnia subtypes in 427 psychiatrically hospitalized children with autism spectrum disorder (mean age = 12.8 ± 3.4; 81.3% male). Per parent report, 60% (n = 257) of children had at least one type of insomnia. The distribution of subtypes was difficulty falling asleep (26.1%, n = 67), difficulty staying asleep (24.9%, n = 64), early morning awakening (4.3%, n = 11), and multiple insomnia symptoms (44.7%, n = 115). Difficulty staying asleep and early morning awakenings were associated with longer hospital stays. Early morning awakening was also associated with higher autism symptom severity. In general, children with difficulty staying asleep or multiple insomnia symptoms scored lower on adaptive behaviors (e.g. communication, self-care, socialization) and higher on maladaptive behaviors (e.g. irritability, hyperactivity, emotional reactivity, and emotional dysphoria). Difficulty staying asleep or having multiple insomnia symptoms appears to be most strongly related to impaired behavioral functioning. Conversely, early morning awakenings may be more closely tied with autism spectrum disorder itself. Further research is needed regarding insomnia subtypes at the severe end of the autism spectrum.