Purpose: To analyze the characteristics of pediatric inflammatory bowel disease (IBD) over the past three decades in Argentina and determine if there are differences between the first two decades and the past decade. Methods: We conducted a retrospective multicenter analytical study in children with IBD between 0 and 18 years of age diagnosed between 1987 and 2017 in three tertiary health centers in Argentina. The evaluation included clinical characterization, endoscopy, histology, and imaging data together with therapeutic strategies. The patients were divided into two groups: Group 1, diagnosed between 1987 and 2007, and Group 2, diagnosed between 2008 and 2017. Results: Of the 756 patients included, 409 (54%) had ulcerative colitis (UC), 250 (33%) had Crohn’s disease (CD), and 97 (13%) had IBD-unclassified (IBD-U). The positive family history was 3.8%, which was more frequent among children under two years of age (6.7%). There were no significant differences in clinical presentation and extraintestinal manifestations between periods, with hepatic manifestations being the most frequent. In the last decade, we found an upward trend in CD, a downward trend in UC/IBD-U, even after adjustment for socioeconomic status, and a decrease of 50% in surgical treatments coinciding with the advent of biological therapy. Conclusion This is the first multicenter cohort study in a Latin American country to describe clinical, endoscopic, and therapeutic data across the past 30-year period. Although CD was responsible for the overall increase in incidence, UC was still prevalent in this region.