Muscles are crucial for balance and walking, activities which depend specifically on the lower extremity muscles. Therefore, the evaluation of stroke induced atrophy and paralysis is essential; however, determining the extent of damage in the days after its occurrence remains challenging. In this study, we evaluated ischemic stroke-induced soleus muscle damage in gerbils using synchrotron radiation X-ray micro-computed tomography (SR-µCT), comparing a control group (n = 3), animals 7 days after stroke (7 d, n = 3), and animals 14 days after stroke (14 d, n = 3). The left muscle was paralyzed, whereas the right muscle was not. Subsequently, we quantified the assessment by segmenting the soleus muscle based on the extracellular space/matrix and fiber region to determine the degree of damage. The muscle fiber-to-extracellular space/matrix ratio were significantly damaged due to paralysis on the left side (control vs. 14 d, P = 0.040). Muscle area was significantly different at 14 d between the left and right sides (P = 0.010). Additionally, the left local fascicle surface area, thickness, global pennation angle, and local fascicle angle were significantly different between the control and 14 d groups (P = 0.002, P = 0.007, P = 0.005, and P = 0.014 respectively). These findings underscore the potential of post-stroke animal studies in improving rehabilitation treatment for the central nervous system by assessing the degree of muscle recovery.