Introduction Duplication cyst of the alimentary tract is a rare congenital anomaly. Duodenal duplication cyst accounts for less than 5% overall. These entities rarely present in adults. They are often mistaken as choledochoceles. Management is most often complete excision, but it is individualized to the particular case. Case presentation A 22-year-old woman was admitted to our hospital with a history of intermittent colicky right hypochondrial pain not relieved by any medications for the past 3 months. Initially, she was given proton pump inhibitors, but her pain was not relieved. Further evaluation was done, and preoperative imaging showed a cyst in the second part of the duodenum. Magnetic resonance imaging revealed it as a choledochocele, but duodenal duplication cyst was kept in the differential diagnosis. Further ultrasound identified it to be a duplication cyst. After failed endotreatment, the patient was successfully managed with partial excision and marsupialization. Conclusion Duodenal duplication cyst is uncommon and rarely diagnosed in adults. Duplications in the duodenum should always be a part of the differential diagnosis, especially in cystic lesions. Ultrasonogram of the cyst might lead to the proper diagnosis. Surgery is the treatment of choice if endotherapy is not successful.