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Background The risk of hepatocellular carcinoma (HCC) in patients with autoimmune hepatitis (AIH) is unclear. We conducted a systematic review and meta-analysis of the incidence of HCC and associated risk factors among patients with AIH. Methods We searched PubMed, Embase, and reference lists from relevant articles through June 2016 to identify cohort studies that examined the incidence of HCC in patients with AIH. We used random effects models to estimate pooled incidence rates overall and in subgroup of patients with cirrhosis. The between-study heterogeneity was assessed using I2 statistic. Results A total of 25 studies (20 papers and 5 abstracts) including 6,528 patients met the eligibility criteria. The median cohort size was 170 AIH patients (range 25–1721 patients) followed for a median of 8.0 years (range 3.3–16.0 years). The pooled incidence rate for HCC in patients with AIH was 3.06 per 1,000 patient-years (95% CI 2.22–4.23, I2 51.5%, p 0.002). The pooled incidence of HCC in patients with cirrhosis at AIH diagnosis was 10.07 per 1,000 patient-years (95% CI 6.89–14.70, I2 48.8%, p 0.015). In addition, 92 of 93 patients that had HCC had evidence of cirrhosis prior to or at time of HCC diagnosis. The risk of HCC appears to be lower in patients with AIH cirrhosis compared to that reported in patients with hepatitis B cirrhosis, hepatitis C cirrhosis, and primary biliary cholangitis. Conclusions Based on elevated HCC risk shown in this meta-analysis, there may be a role for HCC surveillance in patients with AIH cirrhosis.