This study investigated the utility of low-dose computed tomography (ldCT) compared with magnetic resonance imaging (MRI) in diagnosing sacroiliitis in enthesitis-related arthritis (ERA) patients. Thirty patients diagnosed with ERA were evaluated, with a median follow-up of 1.47 years. Imaging data from these patients were examined by two blinded pediatric radiologists. For each patient, we assessed the density changes on ldCT at corresponding locations, employing the signal intensity observed on MRI across each joint surface as a reference. While measurements in areas without edema on MRI showed relatively high density, measurements in areas with edema on MRI showed relatively low density. MRI revealed bilateral bone marrow edema in 22 (73.3%) patients. During the ldCT evaluation of the right iliac crest, lower density was identified on ldCT in regions displaying heightened signal intensity on MRI in 20 (66.6%) patients. On the right sacral side, lower density was observed in the ldCT of 22 (73.3%) patients. Moving to the left iliac crest, 18 (60%) patients displayed a lower density. On the left sacral side, lower density was identified on ldCT in 22 (73.3%) patients. Erosion was detected in 23 patients on ldCT, whereas only 11 patients showed erosion on MRI. This study suggests that ldCT is superior to MRI for early structural change detection. Pixel-based density evaluation in ldCT aligns with MRI findings for bone marrow edema. The present study showed that ldCT is superior to MRI for early structural change detection in pediatric patients. Pixel-based density evaluation in ldCT aligns with MRI findings for bone marrow edema.