Abstract Objective Inflammatory bowel disease is a chronic inflammatory disease of the gastrointestinal tract. Some difficulties and differences were experienced during the coronavirus disease 2019 (COVID-19) pandemic period for monitoring of chronic diseases. In this study, the effect of the COVID-19 pandemic on the frequency and course of inflammatory bowel disease in children was evaluated. Methods The first severe acute respiratory syndrome coronavirus 2 case in Türkiye was diagnosed on March 11, 2020. The pandemic period was defined as the year following this date, and the pre-pandemic period as the preceding year. The number of patients newly diagnosed with inflammatory bowel disease and their clinical presentations during the pandemic period and pre-pandemic period was compared. In addition, the clinical features of previously diagnosed inflammatory bowel disease patients in the pandemic period and pre-pandemic period were compared. Results Eighty-six patients in a pediatric gastroenterology clinic between 2009 and 2021 were included. The number of newly diagnosed patients was higher during the pandemic period (n = 14) compared with the pre-pandemic period (n = 18; p = 0.017). Fifty-four patients were follow-up patients diagnosed before 2019: the mean number of outpatient clinic visits, disease attacks, and hospitalizations was lower pandemic period than pre-pandemic period (p < 0.01). Conclusion The changes experienced during pandemic period may have triggered more cases of inflammatory bowel disease. However, we found no evidence that either less face-to-face follow-up of, or life changes in, existing inflammatory bowel disease patients during the pandemic period adversely affected their clinical outcomes.