This study investigated the effect of a handball-specific fatigue protocol on hip and knee kinematics. Twenty female handball athletes performed three trials of the single-leg landing (SLL), sidestep cutting manoeuvre (SCM), and drop vertical jump (DVJ) before and after the fatigue protocol. Knee and hip angle waveforms were compared using statistical parametric mapping (p < 0.05). During the SLL, the fatigue increased hip adduction (4–7% cycle) and knee abduction (4–9% and 25–27%). For the SCM, hip flexion was reduced under fatigue during 14–29% and 44–68% of the cycle. Similarly, the knee flexion decreased between 7–36% and 53–73%. Besides, during the fatigue state, the athletes reduced the hip abduction between 0–11% of the cycle and increased the knee abduction between 20–23%. During the DVJ task, when fatigued, the hip flexion decreased between 19–44% of the cycle and the knee flexion between 1–16% and 18–77%. The fatigue protocol altered the lower limb kinematics, decreasing knee and hip flexions during the SCM and DVJ and increasing the knee valgus during both single-leg landing tasks.