Autistic children have a high prevalence of co-occurring mental health, developmental/behavioral, and medical conditions, but research on sex/gender differences has been mixed. We used Florida healthcare claims data to characterize sex differences (female/male) in co-occurring conditions among autistic children ages 1–21 (N = 83,500). After adjusting for age, race, ethnicity, urbanicity, and insurance, autistic girls had significantly higher odds of anxiety disorders, mood disorders, intellectual disability, developmental disorders, epilepsy, metabolic disorders, gastrointestinal disorders, and sleep disorders compared to autistic boys. Autistic girls had significantly lower odds of ADHD. The findings contribute to the growing body of research on the unique healthcare needs of autistic girls.