Best practices for scapular motion tracking are still being determined. The repeatability of different scapular kinematic procedures needs to be evaluated. The purpose of this study was to assess the test-retest reliability of two scapular kinematic procedures: double calibration with AMC (D-AMC) and individualized linear modelling (LM). Ten healthy participants had their upper body movement tracked with optical motion capture in two identical sessions. Five scapular calibration poses were performed, and seven dynamic functional tasks were tested. Scapular angles were calculated from both procedures (D-AMC vs LM). The D-AMC approach uses two poses (neutral and maximum elevation) and tracks the scapula with a rigid cluster, while the LM approach predicts scapular positioning from humeral angles based on equations built from the calibration pose data. Angle waveforms and repeatability outcomes were compared. Internal and upward rotation angle waveforms were significantly different (p < 0.05) between kinematic procedures for some tasks, with maximum mean differences up to 17.3° and 23.2°, respectively. Overall, repeatability outcomes were similar between procedures, but the LM approach was slightly better for tilt and the D-AMC approach was notably improved for upward rotation in certain tasks. For example, minimal detectable changes during the Forward Transfer ranged from 6.9° to 11.9° for the D-AMC and 8.9° to 25.3° for the LM. Discrepancies between procedures may be a function of the calibration poses chosen. Additional calibration poses may improve the comparisons between procedures.