The purpose of this work was to investigate whether two-months supplementation with 100% sea buckthorn juice (SBJ) would modify blood lipids, LDL subfractions and other markers of cardiovascular risk in hypercholesterolemic women. A group of 28 hypercholesterolemic non-medicated adult women with a mean age of 50.58 ± 5.76 years consumed 50 mL of 100% SBJ daily for two-months. We observed a significant reduction of body weight (BW; p < 0.05), body mass index (BMI; p < 0.05), body fat mass (BFM; p < 0.001) and visceral fat area (VFA; p < 0.001), on the contrary, a significant increase of skeletal muscle mass (SMM; p < 0.05) and fat-free mass (FFM; p < 0.05). Supplementation with 100% SBJ significantly increased the level of high-density lipoprotein (HDL; p < 0.05), reduced the level of low-density lipoprotein (LDL; p < 0.05), atherogenic LDL subfractions (LDL3–7; p < 0.05) and improved LDL/HDL ratio (p < 0.001). After the SBJ consumption, significant reduction of C-reactive protein (CRP; p < 0.001), orosomucoid (ORM; p < 0.001) and interleukin 6 (IL-6; p < 0.05) were found. In conclusion, consumption of SBJ showed an indication of beneficial effects on cardiovascular risk factors in hypercholesterolemic women.