Inflammatory bowel disease (IBD) includes Crohn’s disease (CD) and ulcerative colitis (UC). These diseases are characterized by inflammation, which may be a consequence of changes in the intestinal microbiota and lead to mineral and vitamin deficiencies. The aims of this study were to determine the level of dietary supplement intake in children with IBD and to determine the influence of factors such as sex, nutritional status, diet, and other comorbidities on supplement intake. The study was conducted from May 2022 to September 2023 and was a prospective study. The group of children with IBD that ultimately qualified for the study numbered 96, and the control group numbered 30. The children who participated in the study were aged 4–18 years. Most parents of children with IBD (81.4%) declared that they use supplementation for their children, while 75% of parents of children without IBD declared giving their children nutritional supplements. Vitamins in both groups were most often given to children as dietary supplements (p = 0.018), including vitamin D. Depending on the diet used, the intake of vitamin B6 (p = 0.018), vitamin E (p = 0.040) and iron (p = 0.006) was significantly different among children with IBD. Statistical significance (p = 0.021) was observed for supplementation use and disease stage among children with IBD. For 80.2% of parents of children with IBD, the main reason for using supplements was a doctor’s recommendation. In the control group, 43.3% of parents indicated that the main reason for using supplements was to correct nutritional deficiencies. Supplementation was common in both groups, but attention should be paid to other current diseases in children with IBD and to nutritional status. In our opinion, educating parents about supplementation is important, especially among parents of children with IBD.