Cerebral venous thrombosis (CVT) is a cerebrovascular disorder caused by complete or partial occlusion of the cerebral venous and sinus system. The etiology has been attributed to hypercoagulability and pro-thrombotic states, leading to raised intracranial pressures that often manifest as headaches and focal neurological deficits. However, the multifactorial nature of CVT can create a diagnostic conundrum for clinicians. We describe a unique case of a 16-year-old female who presented with convulsions, postictal confusion, and drowsiness followed by residual weakness of her extremities. She initially presented to the primary care center with headache, high-grade fever, and altered mental status and was empirically treated for pyogenic meningitis. The patient failed to improve with a week of antibiotics and was referred to the tertiary care center for urgent attention. On presentation, the patient developed VI and VII cranial nerve palsy. Subsequently, MRI images showed filling defects in the superior sagittal, right transverse, and sigmoid sinuses with right parietal gyral T1 hyperintensity and T2 hypo-intensity. She was diagnosed with septic CVT based on sinus venous thrombosis and venous infarction, probably secondary to meningococcal pneumonia. It can be challenging to distinguish between both conditions as their presentations overlap. Moreover, cranial nerve palsy is an infrequent manifestation of CVT, with unclear pathogenesis. We highlight the role of neuro-imaging in the early detection of CVT and bring to light the unfamiliar symptoms and a more varied clinical spectrum that may hinder the diagnosis in a limited-resource setting. Future research should be explicitly modeled to improve the diagnostic efficiency of CVT and improve outcomes in younger patient populations.