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. Lay abstract Autistic individuals experience higher co-occurring medical conditions than the general population, and yet the estimates of autistic individuals with epilepsy are not updated. Co-occurrence of epilepsy in autistic individuals often aggravated cognitive impairment and increased the risk of poor long-term prognosis. Thus, an updated systematic review and meta-analysis was conducted to study the relevant articles published from inception to 2020, evaluate the prevalence of epilepsy in autistic individuals, and further explore the putative factors influencing the prevalence. A total of 66 studies from 53 articles were included in this study. The results showed that epilepsy is more common in autistic individuals than in the general population. The prevalence of epilepsy in autistic individuals in the clinical sample-based studies was higher than that in the population-based based cross-sectional or cohort studies. The prevalence of epilepsy in autistic adults was higher than that in autistic children. A significantly increased prevalence of epilepsy was detected in the autistic adolescent group (11–17 years old), and a higher trend of prevalence of epilepsy was observed in the autistic pre-school group (⩽ 6 -years-old) than that of the autistic school-aged group (7–10 years-old). The prevalence of epilepsy increased with age, female rate, and low intellectual function rate of autistic individuals. However, the human development index of countries was negatively associated with the pooled prevalence, which could be attributed to the different levels of awareness, diagnostic technologies, and autism-service support worldwide. About 1/10 autistic individuals also had 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. Thus, these findings provided critical and innovative views on the prevalence of epilepsy in autistic individuals and contributed to the targeted clinical management and preventive measures.