Thrombosis of the deep cerebral venous system in the absence of superficial sinus thrombosis is a very rare disease. The clinical and radiological findings can be diagnostically challenging due to the subtle appearances on computed tomography (CT) scan. Magnetic resonance imaging (MRI) examination is a preferred imaging modality to complement the CT findings for an accurate diagnosis of venous sinus thrombosis. We present a case of this unusual condition which present as unilateral thalamic lesion on CT scan and the role of contrast enhanced MRI with fast spoiled gradient echo (FSPGR) sequence and 3D reconstruction which led to the diagnosis of thrombosis in the deep cerebral venous system.