The aim of this study was to evaluate the level of agreement in measuring back squat kinematics between an inertial measurement unit (IMU) and a 3D motion capture system (3DMOCAP). Kinematic variables included concentric peak velocity (CPV), concentric mean velocity (CMV), eccentric peak velocity (EPV), eccentric mean velocity (EMV), mean propulsive velocity (MPV), and POP-100: a proprietary variable. Sixteen resistance-trained males performed an incrementally loaded one repetition maximum (1RM) squat protocol. A series of Pearson correlations, 2 × 4 RM ANOVA, Cohen’s d effect size differences, coefficient of variation (CV), and standard error of the estimate (SEE) were calculated. A large relationship existed for all variables between devices (r = 0.78–0.95). Between-device agreement for CPV worsened beyond 60% 1RM. The remaining variables were in agreement between devices with trivial effect size differences and similar CV magnitudes. These results support the use of the IMU, regardless of relative intensity, when measuring EMV, EPV, MPV, and POP-100. However, practitioners should carefully select kinematic variables of interest when using the present IMU device for velocity-based training (VBT), as certain measurements (e.g., CMV, CPV) do not possess practically acceptable reliability or accuracy. Finally, the IMU device exhibited considerable practical data collection concerns, as one participant was completely excluded and 13% of the remaining attempts displayed obvious internal error.