In Japan, Saireito and Onpi-to are widely used Japanese herbal medicine in the treatment of chronic kidney disease (CKD), which is a world-wide public health issue. In this review, it has been discussed the beneficial effects of Japanese herbal medicine, including Sairei-to and Onpi-to on multifarious renal damage in progression of CKD, such as mesangial lesion, inflammatory cell infiltration, cytokine expression, reactive oxygen species release, and aldosterone disorder, and then to clarify the mechanism of these herbs at molecular level by examining the effects on various injurious factors. Both Saireito and Onpi-to are effective agents for delaying the progression of CKD.