Background: Anticoagulation therapy following cerebral vein thrombosis (CVT) can improve mortality and morbidity. Vitamin K antagonists are currently the routine oral anticoagulant used for CVT; while by introduction of rivaroxaban, a direct factor Xa inhibitor, the attentions have been deviated toward novel agents, but the evidence is not strong. The current study is aimed to compare the efficacy and safety of rivaroxaban versus warfarin for anticoagulation therapy of CVT. Methods: The current randomized clinical trial has been conducted on 50 patients with CVT among which, 25 ones were randomly allocated to rivaroxaban treatment (20 mg per day for three months) and remained 25 ones to warfarin treatment [adjusted based on international normalized ratio (INR) of 2-3]. The Modified Rankin Scale (mRS) and clinical investigations, including the incidence of seizure, papilledema, intra/extra-cranial bleeding, blurred vision, headache, nausea and vomiting, and death were evaluated at discharge time and within 3 and 6 months following CVT incidence; eventually, two groups were compared. Results: Comparison of mRS scores between the groups revealed significant differences in none of the interval assessments, at the time of admission (P = 0.510), within three months (P = 0.630), and within six months (P = 0.990), while both of the approaches led to significant decrease in mRS scores following both of the treatments (P < 0.001). The comparison of drug-related adverse effects showed insignificant difference between warfarin versus rivaroxaban (P > 0.050). Conclusion: Based on this study, rivaroxaban is an efficacious agent for the treatment of CVT without remarkable adverse effects.