Intradialytic hypotension (IDH) is associated with high mortality. Peripheral vascular resistance and circulating blood volume are important factors in IDH; however, the effects of hemodialysis (HD) on vascular resistance in IDH remain unclear. We herein performed a retrospective observational cohort study to investigate changes in and factors related to vascular resistance during HD. A total of 101 HD patients were divided into two groups (Decreased blood pressure (BP) during HD group: N = 19, Nondecreased BP group: N = 82), and cardiac output was measured with electrical velocimetry (AESCLON) for 3 h. The systemic vascular resistance index (SVRI) was significantly decreased in the Decreased BP group, while the cardiac index was similar in both groups. A multivariate regression analysis identified hypocholesterolemia as a predictor of reduced vascular resistance reactivity during HD. Furthermore, a correlation was found between changes in the SVRI and cholesterol levels in patients with a higher Geriatric Nutritional Risk Index (GNRI) but not in those with a lower GNRI. The present results suggest that hypocholesterolemia contributes to reducing systematic vascular resistance reactivity during HD, which is an important predictor of a reduction in BP during HD. The relationship between hypocholesterolemia and vascular resistance may involve mechanisms other than malnutrition.