To examine the kinematic characteristics of the hip and knee during a single-leg stop-jump task before and after exercise-to-fatigue, and to determine if the fatigue response is gender-dependent. Lower extremity kinematic measurements were taken of male and female subjects while they performed a sports functional task before and after fatigue developed from exhaustive running. Thirty healthy, physically active subjects (15 males and 15 females) Knee and hip joint kinematics were calculated utilizing three-dimensional video analysis. Each subject performed five single-leg stop-jumps before and after an exercise-to-fatigue bout. All subjects underwent a fatigue protocol using the modified Astrand protocol. Fatigue was verified using the Rating of Perceived Exertion along with the subject's heart rate. All data were analyzed using two factor (test x gender) repeated measures ANOVA (P<0.05). Both males and females demonstrated significantly less maximal knee valgus (P=0.038) and decreased knee flexion at initial contact (P=0.009) post-fatigue. No significant differences were identified in hip joint angles between sessions or between sexes. The results show that fatigue developed from exhaustive running alters lower extremity kinematics during a single-leg stop-jump task. The more neutral position in the frontal plane might be an effort to protect the knee. The decrease in knee flexion at initial contact may be an attempt to increase knee stability following fatigue. Our results did not reveal any gender differences in this specific task.