Exercise can improve and maintain neural or muscular function, but the effects of exercise in physiological adaptation to paralysis caused by botulinum toxin A has not been well studied. Twenty-four rats were randomly assigned into control and treadmill groups. The rats assigned to the treadmill group were trained on a treadmill three times per week with the running speed set at 15 m/min. The duration of training was 20 min/session. Muscle strength, nerve conduction study and sciatic functional index (SFI) were used for functional analysis. Treadmill training improved the SFI at 2, 3, and 4 weeks (p = 0.01, 0.004, and 0.01, respectively). The maximal contraction force of the gastrocnemius muscle in the treadmill group was greater than in the control group (p < 0.05). The percentage of activated fibers was higher in the treadmill botox group than the percentage for the control botox group, which was demonstrated by differences in amplitude and area of compound muscle action potential (CMAP) under the curve between the groups (p < 0.05). After BoNT-A injection, treadmill improved the physiological properties of muscle contraction strength, CMAP amplitude, and the recovery of SFI.