Choledochal cysts (CCs) are quite rare and are characterized by anomalous dilations of the biliary tree, mostly due to anomalous pancreaticobiliary junction (APBJ). A less frequent congenital anomaly due to incomplete fusion of pancreatic ducts, pancreas divisum (PD) can complicate the clinical course of CC. Although rare, the coexistence of CC and PD presents significant clinical challenges. With very few documented cases globally, our experience with this case adds to our understanding of this unique condition. This report aims to highlight the complex relationship between these anomalies and underscores the need for heightened clinical awareness and comprehensive management strategies to improve patient outcomes.We present the case of a 27-year-old female patient who was diagnosed with type 1 CC with concomitant PD after recurrent pancreatitis and multiple biliary interventions. Her choledochal cyst was excised with Rouxen-Y hepaticojejunostomy (RYHJ). Histopathological examination confirmed CC with evidence of chronic inflammatory changes but no malignancy. The preoperative hospital stay was three days with an operative duration of 150 minutes and intraoperative blood loss of 210 mL. Postoperatively, the patient was discharged on day 5. The pain score as per the Visual Analog Scale (VAS) was 2 on the day of discharge. The patient was started on diet on postoperative day (POD) 3. The abdominal drains were removed on POD 4 (subhepatic) and POD 5 (pelvic). Sutures were removed on POD 10, with follow-up for two years with no recurrence of similar complaints. This case illustrates the diagnostic challenge of synchronous CC and PD and elaborates on the role of extensive imaging modalities in guiding management decisions. The surgical approach remains the foremost for CC; preventing complications in the form of cholangitis and malignancy is the mainstay of treatment. The present report is an addition to the existing literature on the management of complex biliary anomalies and places special emphasis on the need for a multidisciplinary approach with individualized treatment strategies in such rare clinical scenarios.Further studies are required to clarify pathophysiological mechanisms linking CC and PD, with the need for better therapeutic strategies toward the optimization of patient outcomes. More studies with robust data are necessary to draw better conclusions.