Differentiating Crohn’s disease (CD) from intestinal tuberculosis (TB) is a challenge. In patients suspected of having CD or intestinal TB compounded with active pulmonary TB in its early stages, clinicians often lean towards a diagnosis of intestinal TB. A 14-year-old female patient was admitted with symptoms of abdominal pain and diarrhea with hematochezia. Colonoscopy revealed a stricture of the ileocecal valve and scattered longitudinal ulcers. Initial chest radiography showed consolidation in the left lower lobe of the lung. Chest CT revealed branching nodular opacities and consolidation. The TB PCR of the bronchial washing fluid was positive. The patient was diagnosed with pulmonary and intestinal TB. The colonoscopy findings favored CD. Despite this, anti-tubercular therapy was initiated based on the radiology findings and PCR test. After treatment with anti-tubercular therapy, the patient’s diarrhea and abdominal pain worsened despite the improvement observed on her chest radiography. Follow-up colonoscopy revealed aggravation of her ulcers. The patient was diagnosed with CD and treated with prednisolone and mesalazine. Her clinical condition improved, and follow-up colonoscopy showed significant improvement of the ulcers. This case highlights the need for caution in diagnosis and suggests that clinicians consider reevaluation in similar cases.