The primary cilium acts as a sensory organelle with diverse receptors and ion channels to detect extracellular cues and regulate cellular functions, including cell migration. The migration of mesenchymal stem cells (MSCs) to bone remodeling sites is important for bone homeostasis. Recently, we have suggested that osteopontin (OPN) is a significant chemoattractant in MSC migration to bone remodeling sites. The objective of this study was to determine whether the primary cilium acts as a chemoattractant sensory unit to detect OPN cues and control MSC migration. We found that the loss of primary cilium induced by silencing of IFT88 reduced OPN-induced migration of MSCs. The effect of IFT88 silencing on cellular attachment, spreading, and proliferation was negligible. The loss of primary cilium did not affect the level of integrinβ1 or CD44, two known receptors for OPN. Interestingly, CD44 was localized to the primary cilium by OPN stimulus. Knockdown of IFT88 or CD44 dysregulated OPN-induced signaling activation and abolished OPN-induced Cdc42 activation. Our findings suggest that the primary cilium acts as a chemoattractant sensor for OPN to regulate MSC migration by controlling not only CD44-mediated OPN signaling, but also Cdc42-mediated actin cytoskeleton rearrangement.