Crohn's disease (CD) has various clinical manifestations, including anal fistulae and perianal abscesses. While perianal abscesses typically occur during infancy, pediatricians should remain alert to the possibility of CD when perianal abscesses appear outside the usual age of onset. We report the case of a three-year-old boy with refractory anal fistulas who exhibited no gastrointestinal symptoms or growth failure at presentation. Gastrointestinal endoscopy revealed no significant mucosal abnormalities, but histopathological examination identified noncaseating epithelioid cell granulomas in the terminal ileum. Based on the presence of characteristic perianal lesions and these granulomas, the patient was diagnosed with CD. Partial enteral nutrition (PEN) therapy led to significant improvement in the anal fistulas. CD presenting solely with perianal fistulas and no luminal involvement is rare, particularly in young patients. This case underscores the importance of histopathological evaluation, including step biopsies, in patients with anal fistulas, even in the absence of gastrointestinal symptoms or endoscopic abnormalities. Additionally, it highlights the potential efficacy of PEN therapy for managing perianal fistulas without luminal involvement, as demonstrated by the patient's marked improvement with this approach alone.