Neuromuscular electrical stimulation (NMES) is often used to increase muscle strength and functionality. Muscle architecture is important for the skeletal muscle functionality. The aim of this study was to investigate the effects of NMES applied at different muscle lengths on skeletal muscle architecture. Twenty-four rats were randomly assigned to four groups (two NMES groups and two control groups). NMES was applied on the extensor digitorum longus muscle at long muscle length, which is the longest and stretched position of the muscle at 170° plantar flexion, and at medium muscle length, which is the length of the muscle at 90° plantar flexion. A control group was created for each NMES group. NMES was applied for 8 weeks, 10 min/day, 3 days/week. After 8 weeks, muscle samples were removed at the NMES intervention lengths and examined macroscopically, and microscopically using a transmission electron microscope and streo-microscope. Muscle damage, and architectural properties of the muscle including pennation angle, fibre length, muscle length, muscle mass, physiological cross-sectional area, fibre length/muscle length, sarcomere length, sarcomere number were then evaluated. There was an increase in fibre length and sarcomere number, and a decrease in pennation angle at both lengths. In the long muscle length group, muscle length was increased, but widespread muscle damage was observed. These results suggest that the intervention of NMES at long muscle length can increase the muscle length but also causes muscle damage. In addition, the greater longitudinal increase in muscle length may be a result of the continuous degeneration-regeneration cycle.