Shoulder kinematics is a measure of interest in the clinical setting for diagnosis, evaluating treatment, and quantifying possible changes. The aim was to compare shoulder scaption kinematics between symptomatic and asymptomatic subjects by inertial sensors. Methods: Scaption kinematics of 27 subjects with shoulder symptomatology and 16 asymptomatic subjects were evaluated using four inertial sensors placed on the humerus, scapula, forearm, and sternum. Mobility, velocity, and acceleration were obtained from each sensor and the vector norm was calculated from the three spatial axis (x,y,Z). Shoulder function was measured by Upper Limb Functional Index and Disabilities of the Arm, Shoulder, and Hand questionnaires. One way ANOVA was calculated to test differences between the two groups. Effect size was calculated by Cohen’s d with 95% coefficient Intervals. Pearson’s correlation analysis was performed between the vector norms humerus and scapula kinematics against DASH and ULFI results in symptomatic subjects. Results: The asymptomatic group showed higher kinematic values, especially in the humerus and forearm. Symptomatic subjects showed significantly lower values of mobility for scapular protraction-retraction (Cohen’s d 2.654 (1.819–3.489) and anteriorisation-posteriorisation (Cohen’s d 1.195 (0.527–1.863). Values were also lower in symptomatic subjects for velocity in all scapular planes of motion. Negative correlation showed that subjects with higher scores in ULFI or DASH had lower kinematics values. Conclusion: Asymptomatic subjects tend to present greater kinematics in terms of mobility, velocity, and linear acceleration of the upper limb, and lower humerus and scapula kinematics in symptomatic subjects is associated with lower levels of function.