The administration of chemotherapy to cancer patients with organ dysfunction raises concerns regarding its safety. The safety profile of patients with organ dysfunction due to rare diseases treated with chemotherapy plus immune checkpoint inhibitor is limited. Fibrinogen storage disease (FSD) is a rare disease that causes liver dysfunction through endoplasmic reticulum stress response due to abnormal accumulation of fibrinogen in the endoplasmic reticulum of hepatocytes. Although chemotherapy plus nivolumab is recommended as a standard first-line treatment for patients with advanced gastric cancer (AGC), its safety profile for patients with FSD is rarely available. In this study, an 80-year-old male with gastric cancer with positive lavage cytology was scheduled to receive palliative chemotherapy. This case had liver dysfunction of unknown cause, and a liver biopsy was performed. Histopathological findings revealed a diagnosis of type II/III fibrinogen inclusion based on morphology and immunohistochemistry. Liver function was recovered by administering ursodeoxycholic acid. Therefore, the combination chemotherapy of S-1, oxaliplatin, with nivolumab as palliative chemotherapy was initiated. The case responded well to chemotherapy and achieved conversion surgery without worsening of liver function. We report a case of AGC with fibrinogen inclusion complication where chemotherapy was safely administered with a good outcome. The combination therapy of cytotoxic drugs and immune checkpoint inhibitors may be safely and effectively administered to such patients.