Enteritis cystica profunda (ECP) is a rare benign condition characterized by mucin-filled cystic spaces in the submucosal layer of the small intestine. It is often associated with inflammatory conditions, such as Crohn's disease. This case report describes a 47-year-old male with a history of diabetes and hypertension who presented with flank pain and dysuria. Imaging revealed a mesenteric mass, which led to a differential diagnosis that included malignancies. Despite extensive evaluations, including computed tomography (CT) scans, positron emission tomography (PET) scans, and colonoscopies, the mass showed no significant changes over time. Six months after the initial presentation, the patient returned with acute abdominal pain and signs of bowel obstruction. Surgical intervention revealed a cauliflower-shaped mass at the root of the mesentery, necessitating resection of the small bowel and cecum. Histopathological analysis confirmed ECP. Postoperatively, the patient developed abdominal collections but responded well to treatment, including antibiotics and interventional radiology. This case underscores the diagnostic challenges of ECP, particularly its potential to mimic malignancies, complicating its management in patients with underlying gastrointestinal (GI) diseases. Enhanced awareness and understanding of ECP are crucial for timely diagnosis and appropriate surgical intervention to prevent complications. Continued research is necessary to refine management strategies for this rare condition.