In the analysis of the shoulder complex, the sequential changes occurring in the sternoclavicular and acromioclavicular joints during active shoulder motion are challenging to track. This study aimed to investigate the in vivo sternoclavicular and acromioclavicular joint motions during active elevation, including the sequential changes in these joint spaces using upright four-dimensional computed tomography (4DCT). Bilateral shoulders of 12 healthy volunteers upright 4DCT were obtained during active elevation similar to a “hands up” motion. The sternoclavicular and acromioclavicular rotation angles, joint distances, and closest points on the clavicle relative to the thorax and scapula were evaluated during 10°−140° of humerothoracic elevation. During humerothoracic elevation, the clavicle elevated, retracted, and rotated posteriorly relative to the thorax, whereas the scapula rotated upwardly, internally, and posteriorly relative to the clavicle. All the sternoclavicular and acromioclavicular joint rotation angles were significantly different at ≥ 30°−50° of humerothoracic elevation compared with 10° of humerothoracic elevation. The mean sternoclavicular and acromioclavicular joint distances were 2.2 ± 1.1 mm and 1.6 ± 0.9 mm, respectively. The closest points were located on the anteroinferior part of the medial and lateral clavicle in the sternoclavicular and acromioclavicular joints, respectively. Significant differences were observed in the acromioclavicular joint distance and anterior/posterior movements of the closest points in the sternoclavicular and acromioclavicular joints compared with 10° of humerothoracic elevation. Our sternoclavicular and acromioclavicular closest point results indicate that the impingement tends to occur at the anteroinferior part of the medial and lateral aspects of the clavicle and may be related to osteoarthritis.