An increased understanding of the relationship between structural connections and functional and behavioral outcomes is an essential but under-explored topic in neuroscience. During transcranial direct current stimulation (tDCS)-induced analgesia, neuromodulation occurs through a top-down process that depends on inter-regional connections. To investigate whether variation in anatomical connectivity explains functional and behavorial outcomes during neuromodulation, we first combined tDCS and a tonic pain model with concurrent arterial spin labelling that measures cerebral perfusion related to ongoing neural activity. Left dorsolateral prefrontal cortex (L-DLPFC) tDCS induced an analgesic effect, which was explained by reduced perfusion to posterior insula and thalamus. Second, we used diffusion imaging to assess white matter structural integrity between L-DLPFC and thalamus, two key components of the neuromodulatory network. Fractional anisotropy of this tract correlated positively with functional and behavioral modulations. This suggests structural dependence by the neuromodulatory process to induce analgesia with potential relevance for patient stratification.