Background <p>Although nociceptive trigeminal input is processed and integrated across multiple regions of the brainstem, thalamus, cerebellum, and cortex, the large-scale functional network organization of these regions, and its relevance to migraine, remain incompletely characterized in humans. Here, we investigated whether a data-driven and hypothesis-guided approach could identify a resting-state functional network centered on the dorsal medulla, the expected anatomical location of the spinal trigeminal nucleus, and whether such a network would be associated with trigeminal pain sensitivity or migraine. We hypothesized that this network would include the thalamus in addition to the dorsal medulla and sought to determine whether it could be reproducibly identified in an independent cohort.</p> Methods <p>Resting-state functional magnetic resonance imaging data were acquired in two independent cohorts. Cohort I comprised 71 healthy participants, and Cohort II comprised 33 healthy participants and 30 patients with episodic migraine in the interictal state. Trigeminal heat pain thresholds were assessed in Cohort I. Masked independent component analysis (mICA), constrained to the brainstem, was first applied in Cohort I to identify networks including the dorsal medulla and thalamus and their associations with trigeminal pain thresholds. Spatially constrained ICA was subsequently applied in Cohort II to evaluate network reproducibility, group differences, and associations with migraine-related measures.</p> Results <p>Using mICA, we identified a network encompassing the full rostrocaudal extent of the dorsal medulla, multiple loci within the pons, midbrain, and thalamus, as well as cerebellar and cortical regions. Connectivity between this network and key regions of the ventral sensorimotor network was positively associated with trigeminal heat pain thresholds. In Cohort II, the core brainstem and thalamic components of this network were reproducibly identified. Furthermore, patients with migraine exhibited reduced connectivity within a dorsal medullary locus (small-volume corrected cluster, P_FDR = 0.004, cluster size = 29), and connectivity within this region was positively associated with headache frequency (<i>N</i> = 30, <i>r</i> = 0.438, uncorrected <i>P</i> = 0.016) and migraine disability scores (<i>N</i> = 30, <i>r</i> = 0.370, uncorrected <i>P</i> = 0.044).</p> Conclusions <p>These findings identify a reproducible brainstem-centered functional network associated with trigeminal pain sensitivity and alterations in migraine. We propose that the anatomical substrate of this network constitutes a functionally connected trigemino-cerebellar system likely involved in sensorimotor integration.</p> Clinical trial number <p>Not applicable.</p>