Shoulder kinematics and muscle activity vary depending on the elevation plane of the upper limb. However, how muscle coordination, which plays a crucial role in controlling shoulder kinematics, differs among elevation planes remains unclear. This study compared shoulder kinematics, muscle synergies, and muscle activation levels across different elevation planes to better understand the neuromuscular mechanisms underlying shoulder kinematics. Shoulder kinematics and muscle activity were recorded during three upper limb elevation tasks (sagittal, scapular, and frontal plane elevation) in 12 subjects (7 males and 5 females). Muscle synergies were extracted using nonnegative matrix factorization, and individual muscle activity levels were calculated as a percentage of maximum voluntary contraction. Glenohumeral elevation was greatest during the sagittal plane elevation task and smallest during the frontal plane elevation task (maximum difference of 14.1°). The differences in kinematics among these elevation planes were suggested to be attributable to the early-stage activity level during elevation of one of the two extracted muscle synergies—specifically, the synergy believed to contribute to humeral head stabilization—and the activation amplitude of the anterior deltoid. Differences in scapular kinematics among three elevation plane tasks could not be explained by variations in muscle synergies but were instead suggested to result primarily from differences in the activation amplitudes of the three parts of the trapezius. To results suggest that shoulder kinematics are controlled by subtle changes in muscle synergy activation patterns and individual muscle activation levels.