Background: Cerebral venous sinus thrombosis (CVST) is defined as the formation of a blood clot within the cerebral venous drainage system. Its incidence is approximately 11.6 cases per 1 million population, and it occurs about twice as often in women as in men. Mortality and disability are reported in 20–25% of patients. Headache is the most common presenting symptom; therefore, differential diagnosis based on pain intensity, location, and clinical examination is essential. Case presentation: In this case, early diagnosis was established using MR venography, and timely, appropriate treatment led to successful dissolution of a thrombus in the sagittal sinus, preventing potential complications and long-term disability. Treatment included high-dose unfractionated and low-molecular-weight heparin administered parenterally, resulting in symptom relief, reduced headache intensity, and improvement in orientation and self-care ability. Prolongation of aPTT seconds indicated a favorable therapeutic response. Subsequently, the patient was transitioned to oral anticoagulant therapy with rivaroxaban (Xarelto) 20 mg. To improve the diagnosis of CVST, the implementation of MR venography and CT venography is recommended in Darkhan-Uul province. Conclusion This is the first case of CVST diagnosed in Darkhan-Uul province, suggesting that further cases may occur. Because headache is the most common presenting symptom, differential diagnosis based on its intensity, character and clinical examination is essential. Early diagnosis with MR venography and timely anticoagulation resulted in recanalization of the superior sagittal sinus and prevented complications and disability. MR and CT venography should be introduced for the diagnosis of CVST in Darkhan-Uul province.