Abstract The aim of this study was to compare the effects of electrical stimulation by using rectangular and sine waveforms in the prevention of deep muscle atrophy in rat calf muscles. Rats were randomly divided into the following groups: control, hindlimb unloading (HU), and HU plus electrical stimulation (ES). The animals in the ES group were electrically stimulated using rectangular waveform (RS) on the left calves and sine waveform (SS) on the right calves, twice a day, for 2 weeks during unloading. HU for 2 weeks resulted in a loss of the muscle mass, a decrease in the cross-sectional area of the muscle fibers, and overexpression of ubiquitinated proteins in the gastrocnemius and soleus muscles. In contrast, electrical stimulation with RS attenuated the HU-induced reduction in the cross-sectional area of muscle fibers and the increase of ubiquitinated proteins in the gastrocnemius muscle. However, electrical stimulation with RS failed to prevent muscle atrophy in the deep portion of the gastrocnemius and the soleus muscles. Nevertheless, electrical stimulation with SS attenuated the HU-induced muscle atrophy and the up-regulation of ubiquitinated proteins in both gastrocnemius and soleus muscles. This indicates that SS was more effective in the prevention of deep muscle atrophy than RS. Since the skin muscle layers act like the plates of a capacitor, separated by the subcutaneous adipose layer, the SS can pass through this capacitor more easily than the RS. Hence, SS can prevent the progressive loss of muscle fibers in the deep portion of the calf muscles.