Abnormal pain processing in the central nervous system may be related to abdominal pain in patients with Crohn's disease (CD). The purpose of this study was to investigate changes in resting-state brain activity in CD patients in remission and its relationship with the presence of abdominal pain. Twenty-five CD patients with abdominal pain, 25 CD patients without abdominal pain, and 32 healthy subjects were scanned using a 3.0 T functional magnetic resonance imaging (fMRI) scanner. Regional homogeneity (ReHo) was used to assess resting-state brain activity. Daily pain scores were collected 1 week before fMRI scanning. We found that patients with abdominal pain exhibited lower ReHo values in the insula, middle cingulate cortex (MCC), and supplementary motor area, and higher ReHo values in the temporal pole. In contrast, patients without abdominal pain exhibited lower ReHo values in the hippocampal/parahippocampal cortex and higher ReHo values in the dorsomedial prefrontal cortex (all P<0.05, corrected). The ReHo values of the insula and MCC were significantly negatively correlated with daily pain scores for patients with abdominal pain (r=−0.53, P=0.008, and r=−0.61, P=0.002, respectively). These findings suggest that resting-state brain activities are different between remissive CD patients with and without abdominal pain, and that abnormal activities in insula and MCC are closely related to the severity of abdominal pain.