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Occult Crohn’s disease in childhood and adolescence remains a diagnostic challenge in clinical practice. The atypical presentation of the disease, including rare extraintestinal manifestations that may overshadow the extent of intestinal inflammation and damage, often complicates clinical assessment. Consequently, the persistent underestimation of alarm features may delay the diagnosis for several years. Aiming to provide clinical, diagnostic and therapeutic insights into the interplay of rare co-occurring disease entities, we present the instructive diagnostic journey of an adolescent with recurrent osteomyelitis finally diagnosed with smouldering inflammatory bowel disease. The challenging interpretation of ambiguous initial findings suggestive of septic osteomyelitis, as well as the routine clinical emphasis on ruling out this condition, had delayed its proper clinical management. Ultimately, the multidisciplinary work-up established the diagnosis of chronic non-bacterial osteomyelitis, a rare extraintestinal manifestation of Crohn’s disease—particularly in childhood-onset cases—and guided the initiation of appropriate treatment, resulting in sustained remission after 2 years of follow-up.