Background: Faecal calprotectin (FCP) is a powerful tool to predict inflammatory bowel disease (IBD) in patients with gastrointestinal symptoms. In the paediatric patient population, the reference value of < 50 μg/g and the influence of age on FCP levels result in a high number of redundant investigations and specialist referrals. We assessed paediatric FCP levels, their diagnostic value and corresponding referral pathways from primary and secondary care. Methods: We analysed two cohorts from a precisely defined catchment area: one consisted of all FCPs measured in this area (n = 2788). The second cohort—a subset of the first cohort—consisted of FCP values and corresponding clinical data from children who were referred for possible IBD to our department (n = 373). Results: In the first cohort, 47% of FCP levels were > 50 μg/g, 15% were ≥ 250 μg/g. Children < 1y had significantly (p < 0.001) higher FCP than older children. In the second cohort, 6.7% of children with an FCP of < 250 μg/g (or 8.6% with an FCP of < 600 μg/g) had IBD–all featured symptoms suggestive of IBD (e.g. bloody diarrhoea, nocturnal abdominal pain, weight loss) or abnormal blood tests. 76% of patients in whom raised FCP (> 50 μg/g) was the sole reason for being referred for suspected IBD did not have IBD. Conclusion: Children with an FCP < 600 μg/g and without matching symptoms suggestive of IBD are unlikely to have IBD. A higher FCP reference value may provide cost-effective improvement that could avoid redundant investigations and specialist referrals. A guideline for specialist referrals is proposed.