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While it is well established that the isoform 2 of the hyperpolarization-activated cyclic nucleotide-gated cation channel (HCN2) plays an important role in the development and maintenance of pain, the role of the closely related HCN4 isoform in the processing of nociceptive signals is not known. HCN4 channels are highly expressed in the thalamus, a region important for stimulus transmission and information processing. We used a brain-specific HCN4-knockout mouse line (HCN4-KO) to explore the role of HCN4 channels in acute nociceptive processing using several behavioral tests as well as a multimodal magnetic resonance imaging (MRI) approach. Functional MRI (fMRI) brain responses were measured during acute peripheral thermal stimulation complemented by resting state (RS) before and after stimulation. The data were analyzed by conventional and graph-theoretical approaches. Finally, high-resolution anatomical brain data were acquired. HCN4-KO animals showed a central thermal, but not a mechanical hypersensitivity in behavioral experiments. The open field analysis showed no significant differences in motor readouts between HCN4-KO and controls but uncovered increased anxiety in the HCN4-KO mice. Thermal stimulus-driven fMRI (s-fMRI) data revealed increased response volumes and response amplitudes for HCN4-KO, most pronounced at lower stimulation temperatures in the subcortical input, the amygdala as well as in limbic/hippocampal regions, and in the cerebellum. These findings could be cross-validated by graph-theoretical analyses. Assessment of short-term RS before and after thermal stimulation revealed that stimulation-related modulations of the functional connectivity only occurred in control animals. This was consistent with the finding that the hippocampus was found to be smaller in HCN4-KO. In summary, the deletion of HCN4 channels impacts on processing of acute nociception, which is remarkably manifested as a thermal hypersensitive phenotype. This was mediated by the key regions hypothalamus, somatosensory cortex, cerebellum and the amygdala. As consequence, HCN4-KO mice were more anxious, and their brain-wide RS functional connectivity could not be modulated by thermal nociceptive stimulation.