Purpose To compare prospective motion correction (PMC) and retrospective motion correction (RMC) in Cartesian 3D-encoded MPRAGE scans and to investigate the effects of correction frequency and parallel imaging on the performance of RMC. Methods Head motion was estimated using a markerless tracking system and sent to a modified MPRAGE sequence, which can continuously update the imaging FOV to perform PMC. The prospective correction was applied either before each echo train (before-ET) or at every sixth readout within the ET (within-ET). RMC was applied during image reconstruction by adjusting k-space trajectories according to the measured motion. The motion correction frequency was retrospectively increased with RMC or decreased with reverse RMC. Phantom and in vivo experiments were used to compare PMC and RMC, as well as to compare within-ET and before-ET correction frequency during continuous motion. The correction quality was quantitatively evaluated using the structural similarity index measure with a reference image without motion correction and without intentional motion. Results PMC resulted in superior image quality compared to RMC both visually and quantitatively. Increasing the correction frequency from before-ET to within-ET reduced the motion artifacts in RMC. A hybrid PMC and RMC correction, that is, retrospectively increasing the correction frequency of before-ET PMC to within-ET, also reduced motion artifacts. Inferior performance of RMC compared to PMC was shown with GRAPPA calibration data without intentional motion and without any GRAPPA acceleration. Conclusion Reductions in local Nyquist violations with PMC resulted in superior image quality compared to RMC. Increasing the motion correction frequency to within-ET reduced the motion artifacts in both RMC and PMC.