This study investigated the effects of knee localised muscle damage on running kinematics at varying speeds. Nineteen young women (23.2 ± 2.8 years; 164 ± 8 cm; 53.6 ± 5.4 kg), performed a maximal eccentric muscle damage protocol (5 × 15) of the knee extensors and flexors of both legs at 60 rad · s(-1). Lower body kinematics was assessed during level running on a treadmill at three speeds pre- and 48 h after. Evaluated muscle damage indices included isometric torque, muscle soreness and serum creatine kinase activity. The results revealed that all indices changed significantly after exercise, indicating muscle injury. Step length decreased and stride frequency significantly increased 48 h post-exercise only at the fastest running speed (3 m · s(-1)). Support time and knee flexion at toe-off increased only at the preferred transition speed and 2.5 m · s(-1). Knee flexion at foot contact, pelvic tilt and obliquity significantly increased, whereas hip extension during stance-phase, knee flexion during swing-phase, as well as knee and ankle joints range of motion significantly decreased 48 h post-exercise at all speeds. In conclusion, the effects of eccentric exercise of both knee extensors and flexors on particular tempo-spatial parameters and knee kinematics of running are speed-dependent. However, several pelvic and lower joint kinematics present similar behaviour at the three running speeds examined. These findings provide new insights into how running kinematics at different speeds are adapted to compensate for the impaired function of the knee musculature following muscle damage.