Background: Gallbladder agenesis is an extremely rare congenital condition in which most patients will remain asymptomatic; nonetheless, a small subset of patients will mimic biliary, urinary, or gastrointestinal disorders. As a result, if these patients are unaware of their condition, an ultrasound may be needed when they present with right upper abdominal pain, which can be misleading or inconclusive, putting the surgeon and the medical team in a diagnostic and intraoperative dilemma. Case presentation: We present the case of a 36-year-old woman with a history of ventricular septal defect and cleft palate. She presented with abdominal pain to the emergency department. After an ultrasound, cholecystitis was misdiagnosed, and, unfortunately, the medical team did not realize this mistake. As a result, surgery was decided. After additional tests, gallbladder agenesis was diagnosed, and the patient fully recovered. Clinical discussion: Congenital absence of the gallbladder can often pose a dilemma to surgeons when it is diagnosed during surgery. Preoperative diagnosis is highly challenging as it can mimic other pathologies; therefore, the medical team needs to keep this pathology on their list of differential diagnoses to avoid dangerous procedures. Conclusions: Congenital absence of the gallbladder can often pose a dilemma to surgeons when it is diagnosed during laparoscopic cholecystectomy. Since preoperative diagnosis is challenging, communication between radiologists and surgeons is critical in order to provide proper care for any patient.