We present a case of a man presenting with vertigo and nausea who was found to have multifocal infarcts in the posterior circulation on magnetic resonance imaging (MRI). An magnetic resonance angiography (MRA) demonstrated focal widening and central signal dropout in the distal vertebral artery consistent with arterial fenestration. Transcranial Doppler ultrasonography showed turbulent flow and a spike waveform suggestive of an intra-luminal thrombus. This was confirmed by computed tomography (CT) angiography. Following the initiation of dual antiplatelet therapy, the signal abnormalities on transcranial doppler (TCD) resolved suggesting dissolution of the thrombus. This case highlights the diagnostic pitfalls that may arise when relying on only one modality for assessing intracranial vasculature and the importance of clarifying the diagnosis of basilar thrombosis or fenestration.