Hepatolithiasis is a benign disease, where stones are localized proximal to the confluence of hepatic ducts. The clinical picture may differ depending on whether the stones cause complete, partial, or intermittent biliary obstruction. The course can vary from asymptomatic to fatal, thus, early diagnosis and treatment is critical for a good prognosis. The gold standard in imaging is magnetic resonance cholangiopancreatography (MRCP). However, correct diagnosis can be challenging due to atypical clinical picture and laboratory findings. We present a case where hepatolithiasis was misdiagnosed initially due to incomplete reporting and documentation of MRCP. Choledocholithiasis was diagnosed based on initial MRCP, and endoscopic stone extraction was indicated. However, an unusual post-interventional course and signs of obstructive cholangitis led to an endoscopic re-intervention, which confirmed absence of pathology in extrahepatic biliary ducts. The cholangitis recurrence required intensive antibiotic treatment, and CT examination revealed intrahepatic S3 bile duct dilatation. Thus, a re-evaluation of initial MRCP and repeated MRCP confirmed hepatolithiasis. Further, laparoscopic bisegmentectomy was chosen as the definitive treatment due to the location of the lesion. The patient recovered and remained symptom free upon a 12 month follow up.