Trigeminal neuralgia (TN) is a physically and mentally incapacitating disorder characterized by extreme, sporadic, sudden facial pain. TN is associated with the trigeminal sensory pathway, however, the etiology of TN remains unclear. Implementing a graph-theory analysis using diffusion MRI we tested whether whole brain network structural connectivity hierarchies differentiate between TN patients and healthy controls. We found aberrant centrality measures of various brain regions in TN. Specifically, this whole-brain data-driven network analysis was able to depict two major regions of the trigeminal sensory circuit, the brainstem and thalamus, and highlight their dysfunction role in the whole brain network.