The present study investigated the protective and treatment effects of different ginseng fractions against L-NAME–induced renal toxicity in rats. The data obtained demonstrated that L-NAME significantly increased creatinine, urea, KIM-1, and lipocalin-2 levels in serum; and also increased renal MDA and eNOS levels compared with the control group. Three bioactive fractions were newly extracted from ginseng, analyzed by GC-MS analysis, and were examined for antimicrobial, prebiotic, and histological activities. All ginseng fractions improved such histological changes, as reflected by significant reductions in creatinine, urea, KIM-1, and LCN-2 levels in serum, and renal MDA and eNOS contents in tissue homogenate. The water ginseng fraction (WGF) has the highest prebiotic index of 4.7 toward Lactobacillus reuteri, and can improve the renal functions more than butanol ginseng fraction (BGF) and ethanol ginseng fraction (EGF). These three ginseng fractions significantly reversed L-NAME–induced depletion in the TNF-α gene expression level. Interestingly, WGF was able to improve the renal functions more than BGF and EGF. L-NAME led to alterations in the histological structure and functions of renal tissue of rats and ginseng supplementation could offer greater protection against these changes. Moreover, the WGF exhibited superior renoprotection properties when compared with the other two fractions: BGF and EGF, and the reference drug losartan.