The aim of this study was to compare scapular kinematics between men and women during shoulder flexion, scapular plane elevation, and shoulder abduction. Eleven healthy men and 11 healthy women participated in this study. As participants performed shoulder flexion, scapular plane elevation, and abduction at a consistent speed, an electromagnetic motion capture system was used to analyze scapular motion. The change in scapular orientation from its resting position was calculated at 30°, 60°, 90° and 120° of humeral elevation. The study found that scapular upward rotation and posterior tilt angles increased significantly with each successive humeral elevation angle, but less so in women than in men. Scapular internal or external rotation differed significantly according to the plane of elevation, that is the scapula was internally rotated during flexion, with no change during scapular plane elevation, and it was externally rotated during abduction. This variation was more marked in women. This study revealed gender differences in scapular kinematics during shoulder motion. During shoulder elevation, the scapulothoracic joint played a greater role in men than in women, whereas the glenohumeral joint played a greater role in women.