Crohn's disease (CD) is a chronic inflammatory disorder that commonly affects the distal small bowel and proximal large bowel. However, it can involve any part of the gastrointestinal tract (GIT), including the upper GIT. However, upper GIT involvement is often overlooked due to the limited use of upper gastrointestinal (UGI) endoscopy and biopsy for diagnosis. We present a case of a 30-year-old male with an 11-year history of symptomatic CD. Despite multiple normal findings on various endoscopic and imaging evaluations, his symptoms persisted, leading to numerous treatment modifications from Pentasa foam enema to various biologics. Despite this, fecal calprotectin remained elevated. A critical diagnosis was made via video capsule endoscopy, revealing duodenitis and aphthous ulcers, and subsequent esophagogastroduodenoscopy (OGD) with histology confirming focal inflammation consistent with upper GIT CD of the stomach and duodenum. Despite aggressive treatment, the patient's symptoms persisted, necessitating comprehensive nutritional management. This case underscores the diagnostic challenges of upper GIT CD and highlights the importance of thorough endoscopic and histological evaluations for accurate diagnosis and effective management. Additionally, it underscores the usefulness of fecal calprotectin as an indication of inflammation and the relevance of nutritional management in controlling symptoms of upper GIT CD.