Interoceptive fear, which is shaped by associative threat learning and memory processes, plays a central role in abnormal interoception and psychiatric comorbidity in conditions of the gut-brain axis. Although animal and human studies support that acute inflammation induces brain alterations in the central fear network, mechanistic knowledge in patients with chronic inflammatory conditions remains sparse. We implemented a translational fear conditioning paradigm to elucidate central fear network reactivity in patients with quiescent inflammatory bowel disease (IBD), compared to patients with irritable bowel syndrome (IBS) and healthy controls (HC). Using functional magnetic resonance imaging, conditioned differential neural responses within regions of the fear network were analyzed during acquisition and extinction learning. In contrast to HC and IBS, IBD patients demonstrated distinctly altered engagement of key regions of the central fear network, including amygdala and hippocampus, during differential interoceptive fear learning, with more pronounced responses to conditioned safety relative to pain-predictive cues. Aberrant hippocampal responses correlated with chronic stress exclusively in IBD. During extinction, differential engagement was observed in IBD compared to IBS patients within amygdala, ventral anterior insula, and thalamus. No group differences were found in changes of cue valence as a behavioral measure of fear acquisition and extinction. Together, the disease-specific alterations in neural responses during interoceptive fear conditioning in quiescent IBD suggest persisting effects of recurring intestinal inflammation on central fear network reactivity. Given the crucial role of interoceptive fear in abnormal interoception, these findings point towards inflammation-related brain alterations as one trajectory to bodily symptom chronicity and psychiatric comorbidity. Patients with inflammatory conditions of the gut-brain axis may benefit from tailored treatment approaches targeting maladaptive interoceptive fear.