The objective of this study was to explore the changes in running kinematics and economy during running at different intensities 1 and 24 hours after a muscle-damaging bench-stepping exercise. Healthy, physically active adult women were recruited for this study. The subjects' running kinematics, heart rate, gas exchange, minute ventilation, and perceived exertion were continuously recorded during the increasing-intensity running test on a treadmill for different testing conditions: a control condition and 1 and 24 hours after the bench-stepping exercise test. Two muscle damage markers, muscle soreness and blood creatine kinase (CK) activity, were measured before and 24 hours after the stepping exercise. Muscle soreness and blood CK activity were significantly altered (exact p ≤ 0.05, Monte Carlo test) 24 hours after the bench-stepping exercise. The stride length, stride frequency, and support time at different running intensities did not change. Twenty-four hours after the previous step exercise, ankle dorsiflexion in the support phase was significantly higher during severe-intensity running, the range of knee flexion at the stance phase was significantly lower during moderate-intensity running, and knee flexion at the end of the amortization phase was significantly lower during heavy-intensity running compared with the control values (exact p ≤ 0.05, Monte Carlo test). The running economy at moderate and heavy intensities, maximum ventilation, and maximum heart rate did not change. We conclude that, given moderate soreness in the calf muscles 24 hours after eccentric exercise, the running kinematics are slightly but significantly changed without a detectable effect on running economy.