Background and Aims: Inflammatory bowel diseases [IBD] are heterogeneous in the frequency and severity of their flare-ups. We aimed to describe disease activity patterns in a Danish nationwide paediatric IBD cohort. Methods: Paediatric patients [<18 years at diagnosis] with Crohn’s disease [pCD] or ulcerative colitis [pUC] in the study period from 1996 to 2018 were identified in national registers. Disease activity [severe, moderate-to-mild, remission] was assessed at diagnosis according to medications prescribed, hospitalizations, and surgeries. Results: In total, 1965 pCD and 1838 pUC incident patients were included in the cohort. At diagnosis, severe disease activity was found in 87%/80% of pCD/pUC and in addition 6.1% of pUC patients had undergone a colectomy during the first year after diagnosis. Five years after diagnosis, the annual proportions of pCD/pUC with no disease activity were 70%/61%, and 10 years after diagnosis the proportions were 72%/64%. Colectomy was required in 6.1, 12, and 16% of pUC patients after 1, 5 and 10 years. No improvement of disease activity was seen in the proportion of prevalent pCD [N = 2515] and pUC [N = 2428] in the study period 2000–2018 concomitant with the introduction of biological treatment. However, decreasing disease activity was the most common pattern in both pCD and pUC [43 and 47%], respectively. Conclusions: pIBD was characterized by a high proportion of patients with severe activity at diagnosis, followed by an improvement after 5 and 10 years of follow-up. Notably, the proportion of patients with no disease activity was unchanged when biological treatment was introduced and the number of colectomies in pUC remained high.