Cerebral venous thrombosis (CVT), a rare thrombotic event that can cause serious neurologic deficits, has been reported after some ChAdOx1 nCoV-19 vaccinations against coronavirus disease 2019 (COVID-19). However, there are few reports of associations between COVID-19 mRNA vaccination and CVT. We retrospectively analyzed CVT occurrence, time of onset after vaccination, outcomes (recovered/not recovered), and death after COVID-19 vaccination from adverse drug reactions (ADR) reports in VigiBase. A disproportionality analysis was performed regarding COVID-19 mRNA vaccines (BNT162b2 and mRNA-1273) and the ChAdOx1 nCoV-19 vaccine. We identified 756 (0.07%) CVT cases (620 (0.05%) after BNT162b2 and 136 (0.01%) after mRNA-1273) of 1,154,023 mRNA vaccine-related ADRs. Significant positive safety signals were noted for COVID-19 mRNA vaccines (95% lower end of information component = 1.56; reporting odds ratio with 95% confidence interval (CI) = 3.27). The median days to CVT onset differed significantly between the BNT162b2 and ChAdOx1 nCoV-19 vaccines (12 (interquartile range, 3–22) and 11 (interquartile range, 7–16), respectively; p = 0.02). Fewer CVT patients died after receiving mRNA vaccines than after receiving the ChAdOx1 nCoV-19 vaccine (odds ratio, 0.32; 95% CI, 0.22–0.45; p < 0.001). We noted a potential safety signal for CVT occurrence after COVID-19 mRNA vaccination. Therefore, awareness about the risk of CVT, even after COVID-19 mRNA vaccination, is necessary.