Glucagon-like peptide-1 receptor agonists (GLP-1RAs) are increasingly prescribed for glycemic control and weight loss management in type 2 diabetes. Their use, however, is associated with a wide range of gastrointestinal adverse effects like nausea, vomiting, and abdominal discomfort. This case report presents a 59-year-old woman with a previous Roux-en-Y gastric bypass who was prescribed semaglutide, and subsequently developed intussusception with small bowel obstruction and chemical pancreatitis. The patient presented to the emergency department with nausea, vomiting, and epigastric pain. The patient's laboratory and radiographic studies revealed a long segment of small bowel intussusception, resulting in a small bowel obstruction and likely chemical pancreatitis. Laparoscopic surgical intervention was required, ultimately converted to a laparotomy for successful reduction of the intussusception. This case report underscores a potential complication that may be seen in patients prescribed GLP-1RAs with prior gastric Roux-en-Y surgeries. The adverse effect is likely attributable to altered gastrointestinal motility and delayed gastric emptying, mechanisms that may be exacerbated by the combination of bariatric-induced anatomical changes and the pharmacological actions of GLP-1RAs. Given the increasing prevalence of GLP-1RA use, emergency medicine clinicians must remain vigilant for these potential serious adverse effects, particularly in patients with complex gastrointestinal histories to ensure timely diagnosis and intervention.