We report a case of 2X-year-old man with G4 chronic kidney disease (CKD G4). He had a decline in estimated glomerular filtration rate (eGFR) after the initiation of BEP (cisplatin, etoposide, bleomycin) therapy followed by VelP (ifosfamide, cisplatin, vinblastine) therapy for mixed germ cell testicular tumor. The patient’s eGFR did not recover during 59 months after chemotherapy, but showed a tendency to improve after treatment with yojinkodakuto. Yojinkodakuto was prepared by the IPCD (immersing powdered crude drugs) method. The IPCD method was adopted to ensure convenience and good quality prescription herbal medicines. Although eGFR fluctuated after yojinkodakuto treatment, at 3 years, serum creatinine (sCr) and eGFR progressed well, with sCr reducing from 3.98 mg/dL at initiation to 2.6 mg/dL and eGFR increasing from 16 mL/min/1.73 m2 to 25.4 mL/min/1.73 m2. In addition, a long-term eGFR plot analysis confirmed the 3-year improvement trend.