As vaccinations against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continue worldwide, increased rates of venous thrombotic events, mainly as cerebral venous sinus thrombosis (CVST), have been reported following adenovirus vector-based SARS-CoV-2 vaccination. However, few reports have described the occurrence of venous thrombosis after messenger RNA (mRNA)-based vaccination. Here, we describe a case of CVST after a first dose of mRNA-based vaccination that was treated with emergent endovascular mechanical thrombectomy and systemic heparinization.Case Description.A 43-year-old, previously healthy man suffered severe headache and partial seizures affecting the left arm 4 days after receiving the first dose of an mRNA-based SARS-CoV-2 vaccination (FC3661; Pfizer/BioNTech). Computed tomography showed intraparenchymal hemorrhage. Seven days after vaccination, symptoms worsened and he was transferred to our tertiary hospital. Magnetic resonance venography revealed CVST with occlusion of the superior sagittal sinus (SSS) and right transverse sinus (TS). Since no findings suggested thrombosis with thrombocytopenia syndrome, the patient underwent systemic heparinization and emergent mechanical thrombectomy with balloon transluminal angioplasty, a stent retriever and an aspiration catheter. Complete SSS and right TS recanalization were achieved and the patient was discharged without neurological deficits.