Individuals with ASD frequently experience one or more comorbid conditions. Here, we investigate the influence of sex and age—two important, yet understudied factors—on ten common comorbid conditions in ASD, using cross‐sectional data from 4790 individuals with ASD and 1,842,575 individuals without ASD. Epilepsy, ADHD, and CNS/cranial anomalies showed exceptionally large proportions in both male (>19%) and female (>15%), children/adolescents with ASD. Notably, these prevalence rates decreased drastically with age in both males and females. In contrast, the prevalence of schizophrenia increased with age affecting a disproportionately large number of older (≥35 year) adult males (25%), compared to females (7.7%), with ASD. Bowel disorders showed a complex U‐pattern accompanied by changes in sex disparity with age. These results highlight crucial differences between cross‐sectional comorbidity patterns and their interactions with sex and age, which may aid in the development of effective sex‐ and age‐specific diagnostic/treatment strategies for ASD and comorbid conditions. Autism Res 2017, 10: 778–789. © 2017 International Society for Autism Research, Wiley Periodicals, Inc.