Enrollment in Medicaid facilitates access to needed services among transition-age youth on the autism spectrum and youth with intellectual disability (ID). There are long-standing programs to ensure that individuals with ID remain enrolled as they age; similar programs for autistic youth are newer, not as widespread, and may not be as effective. We compared Medicaid disenrollment and re-enrollment between transition-age youth on the autism spectrum, youth with ID, and youth with both diagnoses using a national claims-based prospective cohort study from 2008 through 2012. Autistic youth were most likely to disenroll and least likely to re-enroll. Disenrollment peaked for all three groups at ages 19 and 21. Transition-age youth on the autism spectrum experience more disruptions in access to Medicaid-reimbursed services than youth with ID. More equitable Medicaid enrollment options for autistic individuals are needed to ensure their access to critical health care as they age.