Difficulty initiating or maintaining sleep is common among autistic individuals and co-occurs with internalizing and externalizing symptoms. This study tested associations between subcortical regions implicated in sleep processes and measures of dysregulated sleep initiation/maintenance in autistic and non-autistic 2- to 4-year-olds. The role of co-occurring externalizing and internalizing symptoms in these associations was also evaluated. Participants included 203 autistic (131 males, 72 females) and 92 non-autistic (49 males, 43 females) 2- to 4-year-olds who completed magnetic resonance imaging. A subscale of items from the Children's Sleep Habits Questionnaire, previously shown to be reliable across both autistic and non-autistic children, was used to measure dysregulated sleep initiation/maintenance. Externalizing and internalizing symptoms were evaluated using the Child Behavior Checklist--Preschool. Associations between volumes for nine subcortical structures known to be implicated in sleep were separately modeled. Mediation analyses explored whether such associations could be accounted for by externalizing or internalizing symptoms. Smaller right hypothalamus volume was associated with dysregulated sleep initiation/maintenance in both autistic and non-autistic children. Externalizing (but not internalizing) problems partially mediated this association. Findings implicate the right hypothalamus in sleep initiation and maintenance issues for both autistic and non-autistic young children, supporting prior evidence of its central role in sleep regulation.