The aim of this study was to determine the annual incidence and geographic distribution of pediatric inflammatory bowel disease (IBD) in Croatia. This is a prospective, cohort, multicenter observational study based on the data obtained from the Croatian national registry for children with IBD. Children and adolescents younger than 18 years diagnosed with IBD, in time period between June 1, 2016, and May 31, 2017, were recruited. In total, 51 new cases were identified; 19 Crohn’s disease, 28 ulcerative colitis, and 8 IBD-unclassified. Male preponderance of all 3 types of the disease was noticed. The median age at diagnosis was 14.8 years. The calculated annual incidence of pediatric IBD per 100 000 persons per year was 7.05 (2.63 for Crohn’s disease, 3.87 for ulcerative colitis, and 0.55 for IBD-unclassified). A north to south gradient was observed with almost 2 times higher incidence in the northern region of the country.