In team sports, non-contact ACL and MCL injuries occur during abrupt changes of direction, like turns or cutting manoeuvres. Fatigue affects dynamic neuromuscular control and increases knee injury risk. This study analysed how lower limb joints and centre-of-mass kinematics are affected throughout a high-intensity running protocol involving repeated 180°-turns. Twenty young men (18–23 years, BMI: 20.8–24.4 kg m−2) completed a 5-m shuttle running trial lasting 5 min at an average speed of 75% of their maximum aerobic speed. During the test, cardio-metabolic parameters were obtained, together with joints and centre-of-mass kinematics, using a motion capture system. Kinematic data were compared between the first and the last minute of exercise. Perceived exercise intensity ranged from “hard” to “maximum exertion” and post-exercise lactate concentration ranged from 5.4 to 15.5 mM. The repetition of 180°-turns induced a substantial reduction of hip (−60%, p < .001, large effect) and knee flexion (−40%, p = .003, medium-to-large effect), and an increase of hip adduction and internal rotation (+25–30%, p < .05, medium-to-large effect). Since such movements are factors increasing the likelihood of non-contact knee injuries, we concluded that the prolonged repetition of turns may expose participants to increased risk of ligament failure. Prevention programmes should include discipline-specific neuromuscular training especially in late practices.