Purpose: Previous study showed that female college athletes seem to have greater anterior cruciate ligament (ACL) injury rate compared to female high school athletes. The purpose of this study was to compare the differences of the kinematics, kinetics, and muscle activities of knee and hip joints during vertical stop-jump task in female college and high school basketball players. Methods: Ten female college and seven female high school basketball players participated in this study. Vertical stop-jump movement was captured and analyzed by a 3D electromagnetic motion analysis system synchronized with a force plate. Muscle activities of the knee joint during vertical stop-jump movement was recorded with a surface electromyographic system (EMG). Isokinetic knee muscle strength and isometric hip muscle strength were measured using an isokinetic dynamometer. Results: At the initial foot contact during vertical stop-jump movement, the knee flexion angle and knee abduction moment of high school basketball players were significantly greater compared with college basketball players. At the instant of the maximum posterior ground reaction force (PGRF), high school basketball players had greater knee and hip flexion angle, greater anterior tibia shear force, and greater knee abduction moment compared with college basketball players. There were no significant differences between groups in knee muscle activities during 150 ms prior to the instant of the maximum PGRF. After landing, high school basketball players demonstrated greater knee abduction moment compared to college basketball players. No significant differences in knee and hip muscle strength were observed between the two groups. Conclusion: Compared with female college basketball players, female high school basketball players had greater knee flexion angle and greater knee loadings during vertical stop-jump task.