Hepatolithiasis is the presence of calculi within the intrahepatic bile duct and has various causes, including liver operations. In the presented case, intrahepatic stones were detected in the patient 30 years ago. Three years ago, before visiting our hospital, at the age of 68, a choledojejunal anastomotic operation was performed for the distention of the common bile duct. Intrahepatic calculi also occurred postoperatively. Percutaneous transhepatic biliary drainage and lithotripsy were conducted, but the intrahepatic stones reoccurred. This treatment was performed three times in total, last year. In the patient, hepatobiliary enzymes were elevated over the past year. To prevent hepatolithiasis recurrence, the patient visited the Kampo medicine outpatient department for inchingoreisan and shigyakusan treatment. Prior to treatment, the patient experienced abdominal discomfort in the hypochondrium. Upon treatment, a transient hepatic enzyme elevation occurred, which was assumed to be a paradoxical healing response, and drug administration was suspended. The prescription was resumed after 3 months, upon stabilization of elevated liver enzyme levels. Ten years after treatment, the patient’s condition was stable, without intrahepatic stone recurrence and apparent elevation of hepatobiliary enzymes. Inchingoreisan is reported to suppress calculi. Shigyakusan, free of the occasionally liver-damaging Scutellariae Radix, was also reported to be effective for hypochondrium discomfort. In conclusion, the combination of these treatments is suggested as a useful therapy in this case of hepatolithiasis.