Fatigue is a common and burdensome problem for patients with inflammatory bowel disease (IBD). Previous studies lack insight into the individual variability in fatigue severity and course over time, and the characteristics of patients at risk of severe and persistent fatigue. This study aimed to identify distinct groups of IBD patients based on their level and course of fatigue over five years. Subsequently, we examined the relationship between these trajectories, patient characteristics and trajectories of perceived stress, sleep and physical activity. This longitudinal cohort study used prospectively collected data from the myIBDcoach telemedicine monitoring tool, including 320 IBD patients who completed three or more online consultations between 2016 and 2021. Latent class growth analyses were performed to identify distinct trajectories. We found five subgroups with distinct trajectories of fatigue, differing in level and course over time, with 33% of patients experiencing chronic stable and high levels of fatigue. Few differences in patient characteristics were found between trajectories, yet the chronic high fatigue subgroup was more likely to report persistent stable sleep problems, perceived stress, and little physical activity over time compared to the other groups. Distinct subgroups of IBD patients can be identified based on longitudinal fatigue trajectories. The relatively stable levels of fatigue, stress, sleep, and physical activity suggest that a one-time screening of patients on these topics may be sufficient to identify those at risk. Interventions aiming to reduce fatigue should target persistent stress, sleep problems, and low levels of physical activity.