For a study, researchers sought to understand that HRV, a measure of parasympathetic vagal activity, was significantly lower in patients with inflammatory bowel disease (IBD) than in healthy controls. This study aimed to look at HRV as a predictor of clinical outcomes in children with IBD. It was a study that was conducted in the future. Children (12–18 years old) with IBD were recruited prospectively. Each patient had 2 different 10-minute HRV measurements taken with a photoplethysmograph finger sensor. The square root of the mean squared differences of successive R-R pulse intervals (RMSSD) was calculated as an indirect index of vagal activity. During a 12-month follow-up, clinical data such as demographic variables, disease activity, course, medications, and laboratory results were collected. The relationship between RMSSD and clinical outcomes was investigated after controlling for confounders. A total of 34 children with IBD were included in the study. Patients in clinical remission had a significantly higher RMSSD than patients with active disease (67.72±27.81 versus 45.76±22.04, P=0.022, respectively). Multivariate analysis revealed that a higher RMSSD was a significant and independent predictor of a lower risk of IBD exacerbation (odds ratio=0.941, 95% CI 0.887–0.998, P=0.044). HRV correlates with IBD activity and may be used to predict disease exacerbation in children with IBD.