Adult overhead athletes without a history of shoulder injury show scapular adaptations. There is a lack of detailed assessment of scapular kinematics in junior overhead athletes. This study aims to investigate three-dimensional scapular kinematics in junior overhead athletes. We recruited a total of 20 junior tennis players and 20 healthy children without participation in any overhead sports in this study. Bilateral scapular kinematic data were recorded using an electromagnetic tracking device for scapular plane glenohumeral elevation. The data were further analysed at 30 degrees, 45 degrees, 60 degrees, 90 degrees and 120 degrees during glenohumeral elevation and lowering. Statistical comparisons of the data between groups (junior overhead athletes and non-overhead athletes) and sides (serve dominant and non-dominant shoulders of the overhead athletes) were analysed with the ANOVA. Comparisons showed that, in general, the scapula was more upwardly rotated and anteriorly tilted in overhead athletes when compared to non-overhead athletes, however there was no side-to-side differences when serve dominant and non-dominant shoulders compared in junior overhead athletes. The serve dominant arm of junior overhead athletes had alternations in scapular kinematics when compared with the non-overhead athletes. These findings provide clinical evaluation implications and the need for clinicians to assess for potential adaptations in junior overhead athletes.