Chronic kidney disease is a prevalent and significant disease worldwide. This study investigated the effects of a medicinal probiotic (BIO-THREE, TOA Biopharma Co., Ltd, Tokyo, Japan) with safety assurance that contained Bacillus subtilis TO-A, Enterococcus faecium T-110, and Clostridium butyricum TO-A in chronic kidney disease. BIO-THREE was approved as a medical drug by the Japanese Ministry of Health, Labour and Welfare and is widely used in the human medical field to improve various symptoms caused by abnormal intestinal microflora. Sixty male rats were randomly assigned to three groups: (1) normal group (n = 20, group 1), rats were given a normal diet for 3 weeks, followed by phosphate-buffered solution (once daily, orally) and a normal diet for 4 weeks; (2) control group (n = 20, Group 2), rats were given a normal diet including 0.75% adenine for 3 weeks, followed by phosphate-buffered saline (once daily, orally) and a normal diet for 4 weeks; and (3) probiotic group (n = 20, Group 3), rats were given a normal diet including 0.75% adenine for 3 weeks, followed by probiotics (once daily, orally) and a normal diet for 4 weeks. Probiotic administration resulted in a decrease in intestinal pH by increasing short-chain fatty acid (SCFA) production, and consequently suppressed the production of urea toxin production, thus, protecting renal function. The lower intestinal pH also promoted a reduction in the blood phosphorus levels by promoting ionisation of calcium and its binding to free phosphorus. This probiotic-induced increase in SCFA production reduced intestinal permeability, inhibited blood lipopolysaccharide and urea toxin production, and prevented the weakening of muscle function and strength. Moreover, it improved dysbiosis in the gut. This study shows the potential of this probiotics approved as medicinal drug to reduce chronic kidney disease progression, especially where safety is required. Further studies are warranted to validate these findings in humans.