BACKGROUND Diagnosing cerebral venous thrombosis (CVT) poses significant challenges owing to a nonspecific clinical presentation, poorly correlated laboratory biomarkers, and low sensitivity of non-contrast head computed tomography (CT). We describe a case of missed CVT diagnosis, due to low clinical suspicion and nonrecognition of anemia as a prothrombotic factor, especially during an ulcerative colitis (UC) flare. A recently proposed CVT clinical probability score can guide clinicians in pursuing further neurovascular imaging. CASE REPORT A 35-year-old man, with treatment-naive UC, presented to the Emergency Department (ED) with new-onset diffuse headache, 4 weeks of bloody diarrhea, and weight loss. Initial ED laboratory studies revealed severe anemia and unremarkable non-contrast head CT. Two days later, the patient returned to the ED for worsening headache. Non-contrast head CT revealed a left temporal hypodensity. This was later confirmed as acute ischemia on magnetic resonance imaging (MRI). MR venogram revealed thrombosis of the left transverse and sigmoid sinuses, leading to initiation of therapeutic subcutaneous anticoagulation. Repeat MRI, secondary to worsening headache, revealed the development of petechial hemorrhages within the core of venous ischemia in the left temporal lobe. Therapeutic anticoagulation, along with symptomatic management of UC, led to clinical stabilization. CONCLUSIONS CVT should be suspected in patients with UC, especially in the context of anemia, presenting with new-onset or worsening headaches. Recognizing anemia as a thrombogenic factor is crucial. Diagnosis of CVT is challenging due to non-focal symptoms and poorly correlating diagnostic tests. We endorse implementing the CVT clinical probability score into AHA/ASA CVT guidelines to enhance diagnostic accuracy.