To direct interventions aimed at improving scapular position and motion in shoulder pathologies, a clinically feasible, objective, sensitive and reliable assessment of scapular dyskinesis is needed. The aim of this study is to evaluate the intra- and inter-observer reliability and the precision of 3D scapula kinematics measurement using wireless sensors of an inertial and magnetic measurement system (IMMS). Scapular kinematics during humerus anteflexion and abduction of 20 subjects without shoulder pathologies were measured twice by two observers at two different days, using IMMS. Similar movement patterns and corresponding high intraclass correlation coefficients were found within (intra) and between (inter) observers, especially for scapular retraction/protraction (0.65–0.85) and medio/lateral rotation (0.56–0.91). Lowest reliability and highest difference in range of motion were observed for anterior/posterior tilt. Medio/lateral rotation and anterior/posterior tilt showed a high precision, with standard error of measurement being mostly below 5°. The inter-observer measurements of retraction/protraction showed lowest precision, reflected in systematic differences. This is caused by an offset in anatomical calibration of the sensors. IMMS enables easy and objective measurement of 3D scapula kinematics. Further research in a patient population should focus on clinical feasibility and validity for measurement of scapular dyskinesis. This would include the application of a scapula locator to enhance anatomical calibration.