Abstract Background The aim of this study was to define clusters of activity in a population-based cohort during the first 5 years after diagnosis in children with ulcerative colitis UC and to identify early prognostic risk factors. Methods All UC patients from the SIGENP IBD registry with a complete follow-up of at least 5 years were included. Active disease was defined every 6 months in the presence of at least one of the following: clinical activity Paediatric Ulcerative Colitis Activity Index ≥ 35; endoscopic activity Mayo score ≥ 1; faecal calprotectin > 250 µg/g; hospitalization; surgery; or treatment escalation. Formula-based clusters were generated based on four published questionnaire-based activity patterns in adults, plus one additional cluster. Results In total, 226 patients were identified. Forty-two 19% had moderate–severe chronically active disease, 31 14% chronic–intermittent, 75 33% quiescent, 54 24% active disease in the first 2 years after the diagnosis, then sustained remission, and 24 11% a remission in the first 2 years then an active disease. Mild disease onset along with a lower clinical severity not requiring the use of corticosteroids at 6 months were related to a quiescent disease course at the next follow-up (logistic model area under the curve 0.86 95% confidence interval 0.78–0.94; positive predictive value 67%; negative predictive value 70%). Eight per cent of patients needed surgery, none in the quiescent group p = 0.04. Conclusions More than one-third of children with UC present with a chronically active or intermittent course during the first 5 years of follow-up. A significant group of patients has active disease in the first 2 years and then sustained remission. Interestingly, after initial treatment, one-third of patients have well-controlled disease throughout.