When a cell migrates, the centrosome positions between the nucleus and the leading edge of migration via the microtubule system. The protein CrpF46 (centrosome-related protein F46) has a known role during mitosis and centrosome duplication. However, how CrpF46 efficiently regulates centrosome-related cell migration is unclear. Here, we report that knockdown of CrpF46 resulted in the disruption of microtubule arrangement, with impaired centrosomal reorientation, and slowed down cell migration. In cells that express low levels of CrpF46, stress fibers were weakened, which could be rescued by recovering Flag-CrpF46. We also found that CrpF46 interacted with non-muscle myosin high chain IIA (NMHC IIA) and that its three coiled-coil domains are pivotal for its binding to NMHC IIA. Additionally, analyses of phosphorylation of NMHC IIA and RLC (regulatory light chain) demonstrated that CrpF46 was associated with myosin IIA during filament formation. Indirect immunofluorescence images indicated that NM IIA filaments were inhibited when CrpF46 was under-expressed. Thus, CrpF46 regulates cell migration by centrosomal reorientation and altering the function of the actomyosin network by controlling specific phosphorylation of myosin.