It is important to measure mechanical properties of muscle, since muscle stiffness is an important component of stabilizing or controlling joint stability. The levels of sex hormones especially estrogen vary over the phase of the menstrual cycle and impact the mechanical properties of soft tissue such as muscle, tendon, and ligaments due to the presence of 17-β estradiol receptor in human connective tissues. Recently, shear-wave elastography (SWE), based on ultrasound imaging, has been used as an accurate technique for visualizing and assessing tissue stiffness. The purpose of this study was to compare the muscle stiffness at rest and during contraction condition between the early follicular phase (menstruation) and ovulation in young women, measured using SWE. Thirty-seven young women with regular menstrual cycles completed this study throughout one full menstrual cycle. Stiffness of lower limb muscles such as the rectus femoris, biceps femoris, tibialis anterior, and medial gastrocnemius was measured at resting and during contraction conditions using SWE during menstruation and ovulation. All muscles showed significantly greater stiffness during the menstruation than ovulation when muscles were actively contracted (P < 0.05), whereas no significant differences in muscle stiffness at rest were noted across phase of the menstrual cycle. These significant findings suggest that muscular factors are changed with estradiol fluctuations; muscles are less stiff during ovulation where the levels of estradiol peak when muscles in a contraction condition. As muscle stiffness is an important part of joint stability, these differences should be recognized to prevent the risk of musculoskeletal injuries.