The literature from inception to 2020 on the prevalence of epilepsy in autistic individuals was systematically reviewed and further explored by subgroup analyses and meta-regression models. This systematic review is registered with PROSPERO (CRD42020179725). A total of 66 studies from 53 articles were included. The updated pooled prevalence of epilepsy in autistic individuals was 10% (95% CI: 6-14). The respective prevalence estimate of epilepsy was 19% (95% CI: 6-35) in the clinical sample-based cross-sectional study, 7% (95% CI: 3-11) in the cohort study, and 9% (95% CI: 5-15) in the population-based cross-sectional study. The pooled prevalence of epilepsy was 7% (95% CI: 4-11) in autistic children and 19% (95% CI: 14-24) in autistic adults. Compared to the school-aged group, the adolescence group (OR: 1.15, 95% CI: 1.06-1.25) and the pre-school group (OR: 1.06, 95% CI: 0.94-1.19) were positively associated with the prevalence of epilepsy. The moderators of age, human development index of the country, gender, and intellectual function accounted for most of the heterogeneity. The prevalence estimates were associated with age, female gender, intellectual disability rate, and the human development index of countries. About 1/10 autistic individuals co-occurred with epilepsy, which was common in the clinical setting, adolescents, adults, females, or patients with intellectual disability, and less common in the country with high human development index.