Running is popular for its convenience and associated health benefits in wide range of population. However, injuries encountered during running are not uncommon, among which most of are lower limb injuries. One of the factors most associated with foot and ankle running related injuries include anatomical or biomechanical abnormalities. The purpose of the present study is to compare the kinematic and neuromuscular variables during running in individuals with normal or excessive foot pronation. Various kinematic and neuromuscular variables of 16 participants were measured using quintic motion analysis system and wireless electromyography (Myo EMG), respectively, during running on treadmill. The segregation of participants into two groups, normal and excessive pronation, respectively, was done using navicular drop test. Shapiro–Wilk test for normality was performed on all variables which confirms the use of Mann–Whitney two-tailed significance test to verify the difference between two groups. The statistical significance difference was set at p ≤ 0.05. The study concluded that there is no significant difference found in the neuromuscular activities of the selected muscles but found some in the other parameters like ankle joint range of motion, linear acceleration, and pronation angle at mid-stance. The finding of the study suggests that the foot alignment and technique plays an important role in the running.