Abstract Objectives Inflammatory bowel disease (IBD) is an immune‐mediated, chronic, remitting, and relapsing disease. Calprotectin, used in monitoring the disease activity, is expressed from neutrophilic granulocytes during inflammation. Neutrophil gelatinase‐associated lipocalin (NGAL) is strongly expressed in both granulocytes and the intestinal epithelial cell layer. The aim of the study was to compare fecal NGAL (FNGAL) with fecal calprotectin (FCAL) in children with IBD. Methods Forty‐four children with IBD and 22 healthy children were included in the study. The patients were divided into two groups, patients with active disease and remission group. Clinical and demographic characteristics, disease activity scores, and serum and fecal markers of the patients were recorded. Results The mean age of the patients was 13.2 ± 3.4 years (range 6–17 years) and male/female: 0.62. FNGAL levels of patients with active disease were higher than those in the remission group ( p < 0.001). A statistically significant positive correlation was observed between Pediatric Ulcerative Colitis Activity Index scores and white blood cell count, platelets, neutrophil‐to‐albumin ratio (NAR), erythrocyte sedimentation rate (ESR), C‐reactive protein (CRP), and FNGAL. There was a positive correlation between Pediatric Crohn's Disease Activity Index scores and platelets, NAR, ESR, CRP, and FNGAL, whereas there was a statistically significantly negative correlation with activity scores and albumin. While FNGAL had 95.5% sensitivity and 81.8% specificity, FCAL had 86.7% sensitivity and 85.7% specificity. Conclusions FNGAL levels were found to be high and sensitive in determining disease activity in our patients with IBD, suggesting that it may be a valuable biomarker.