Taiwanofungus camphoratus has been widely used in Taiwan as a folk medicine to prevent and treat liver diseases, diarrhea, abdominal pain, itchy skin, and hypertension. Recent studies have shown that T. camphoratus mycelia extracts exert anti-inflammatory and antioxidant effects on some types of renal disease, but the effect of T. camphoratus mycelia on chronic kidney disease (CKD) remains unclear. In this study we used the Bioresource Collection and Research Center (BCRC) medium and modified media (e.g., BCRC+A, HKS1, and HKS1+A media) to incubate T. camphorates mycelia and detect the feasible benefits of renal protection in mice with CKD. Five groups of mice with a partial nephrectomy (each mouse weighed approximately 30 g) received a daily administration of different media-treated T. camphoratus mycelia water solutions (3 mg dried mycelia dissolved in 0.3 mL water) by oral gavage for 30 days, while a control group received distilled water. The results show that progressive increased blood urea nitrogen and serum creatinine were significantly inhibited in the HKS1+A group on days 10 and 30. Plasma total protein was effectively increased in the HKS1 and HKS1+A groups. The BCRC and BCRC+A groups exhibited no obvious improvement in renal function. The results suggest that the HKS1+A medium provides the optimal effect in preventing the deterioration of kidney function and might have a renoprotective effect on CKD.