Background: The faecal calprotectin (FC) measurement is used for inflammatory bowel disease (IBD) diagnosis and follow-up. The aim of this study was to validate for the first time the new IDS FC extraction device and immunoassay kit, and to compare it with the DiaSorin test in patients with and without IBD. Methods: First, the precision of the IDS assay and its stability were assessed. Then, 379 stool extracts were analysed with the IDS kit on iSYS and compared with a DiaSorin Liaison XL assay. Results: The intra- and inter-assay CVs did not exceed 5%. The stool samples were stable up to 4 weeks at −20 °C. Lot-to-lot comparison showed a good correlation (Lot1 = 1.06 × Lot2 + 0.60; p > 0.05). The Passing and Bablok regression showed no significant deviation from linearity between the two methods (IDS = 1.06 × DiaSorin − 0.6; p > 0.05; concordance correlation coefficient = 0.93). According to the recommended cut-offs, the IDS assay identified more IBD and irritable bowel syndrome patients than DiaSorin, which had more borderline results (16 vs. 20%, respectively). Conclusions: The IDS faecal calprotectin had good analytical validation parameters. Compared to the DiaSorin method, it showed comparable results, but slightly outperformed it in the identification of more IBD patients and active disease.