<i>Introduction</i>: Chronic gastrointestinal disorders are common in children. Numerous faecal biomarkers, such as faecal calprotectin, are used in the aetiological diagnosis of these digestive disorders. The study aimed to investigate the diagnostic value of faecal calprotectin in paediatric chronic gastrointestinal disease compared with that obtained in healthy children. <i>Methodology</i>: This was a comparative, analytical cross-sectional study from October 2022 through June 2023 at Yaoundé General Hospital. Participants were children aged between four and eighteen with chronic digestive disorders. Using a pre-established questionnaire, we collected the socio-demographic and clinical characteristics of each participant. The participants' faecal calprotectin was tested at the laboratory of the Yaoundé University Hospital Center by Enzyme-Linked Immunosorbent Assay (ELISA). Associations between variables were investigated by linear regression and calculation of the odds ratio (OR). The significance threshold was 5%. <i>Results</i>: Sixty stool samples were analysed for faecal calprotectin from 30 patients and 30 healthy participants. The mean age of the population was 9.47 (± 3.35) years for patients and 10.67 (± 3.70) years for healthy participants, with a sex ratio of 1.14 for patients and 0.87 for healthy participants. The threshold value for faecal calprotectin was 2.75 µg/g, with a sensitivity of 60%, a specificity of 63%, a positive predictive value of 61.20% and a negative predictive value of 62.06%. There were no significant differences in faecal calprotectin concentrations between children with chronic gastrointestinal disorders (peptic ulcer disease: p=0.10; functional gastrointestinal disorder associated with peptic ulcer disease: p= 0.710; functional gastrointestinal disorder: p= 0.143) and healthy children. <i>Conclusion</i>: The diagnostic value of faecal calprotectin as a biomarker in the diagnosis of chronic gastrointestinal disease was not observed in this study. However, the biological parameters assessed were measured only once, and given that their concentrations may vary over time, we recommend a subsequent longitudinal study.