Motion control shoe is a well developed technology in running shoe design for controlling excessive rearfoot pronation and plantar force distribution. There is, however, little evidence on the lower leg muscle activation response to different shoes. This study examined the shank muscles EMG activity with different footwear. Methods: Twenty female recreational runners with excessive rearfoot pronation were tested with running for 10km on a treadmill on 2 days. Subjects wore either motion control running shoe or neutral running shoe during each day. Activities of their right tibialis anterior (TA) and peroneus longus (PL) were recorded with surface EMG. Their normalized root mean square (RMS) EMG and median frequency (MF) were compared between the two shoe conditions. Results: Significant positive correlations were found between the RMS EMG and running mileage in both TA and PL in the neutral shoe condition (p<0.001). There was MF drop in both shoe conditions with mileage but paired t-tests revealed significantly larger drop in the neutral shoe (p<0.001 for PL, p=0.074 for TA). Conclusions: Motion control shoe may facilitate a more stable activation pattern and higher fatigue resistance of TA and PL in people with excessive rearfoot pronation during running.