Objective: Worldwide the incidence of pediatric Crohn’s disease (CD) and ulcerative colitis (UC) is suspected to be increasing. Based on unselected nationwide register data the aim of this study is to examine the change in incidence of CD and UC in children and adolescents in Denmark. Materials and methods: All children and adolescents <17 years with a diagnosis of CD or UC registered in the Danish National Patient Registry from 1 January 1995 to 31 December 2013 were included. Using a Poisson regression model we estimated the incidence rate ratio (IRR) for the annual change in the incidence adjusted for gender and age. The cumulative incidence was described using Kaplan–Meier survival analyses. Results: The IRR for CD was 1.052 (95% CI: 1.039–1.065), and for UC the IRR was 1.022 (95% CI: 1.011–1.033), adjusted for age and gender. The incidence rate of CD increased during the study period to 10.0 (95% CI: 7.5–13.2) per 100,000 person years for girls and 9.4 (95% CI: 7.0–13.2) for boys, in 2013. Similar, the incidence of UC increased to 7.2 (95% CI: 5.0–9.9) per 100,000 person years for girls and 6.2 (95% CI: 4.3–8.7) for boys. Conclusions: In a period of 19 years from 1995 to 2013 we found an increasing incidence for pediatric UC and CD, especially pronounced for CD.