Choledochal cyst is a rare congenital malformation of the biliary tree. It can be present in various locations along the biliary tree. The diagnosis of choledochal cyst during pregnancy can be challenging for clinicians due to its atypical presentation. In this case report, we discuss a case of a female patient who presented in the third trimester. She was misdiagnosed with cholecystitis and was treated medically. She underwent emergency lower segment cesarean section (LSCS) and was then discharged. The patient later presented with the same symptoms and was diagnosed with choledochal cyst type IVA. She underwent percutaneous drainage and improved. The patient had to deliver the baby prematurely due to the late diagnosis and thus late treatment.In order to avoid the recurrence of those events, physicians should be familiar with the presentation of a choledochal cyst and should subsequently use the proper imaging modalities such as MRI more frequently in pregnant patients with such presentation, which will result in an early diagnosis and prevent the maternal and fetal complications.