Repetitive transcranial magnetic stimulation (rTMS) is an alternative treatment option for patients with drug-resistant trigeminal neuralgia (TN). However, the effect of rTMS is variable. The aim of this study was to find neuroimaging biomarkers of clinical efficacy of navigated rTMS. Seventeen patients with TN (14 women and 3 men, median age 56 years) received 10 sessions of high-frequency rTMS of the motor cortex contralateral to pain side. The data were analyzed for correlations between functional connectivity (FC), the grey matter (GM) volume and the reduction in pain intensity. Positive correlations were established between the reduction in average pain intensity and GM volume in caudate nuclei in both hemispheres (p(unc) = 0.03), both cerebellar hemispheres (p(unc) = 0.002) and the postcentral gyrus contralateral to pain side (p(unc) = 0.005); between the reduction in peak pain intensity and GM volume in the caudate nucleus contralateral to pain side (p(unc) = 0.04) and the cerebellar hemisphere ipsilateral to pain (p(unc) = 0.03). Significant positive correlations were discovered between the reduction in average pain intensity and FC between the thalamus contralateral to pain side, the postcentral gyrus and the insular operculum (both ipsilateral to pain side; (p(FWE) = 0.018), as well as between the cingulate cortex and the anterior cingulate cortex ipsilateral to pain (p(FWE) = 0.017), between the contralateral subcallosal gyrus and the cerebellar hemisphere ipsilateral to pain (p(FWE) = 0.018). A negative correlation was established for FC between the contralateral putamen and the occipital lobes in both hemispheres (p(FWE) = 0.001). Our findings may spur the development of individual predictors of rTMS efficacy in patients with chronic pain.