Bioactive sphingolipid ceramide is a second messenger in cell membrane in response to inflammation and stress. Recent studies indicate that ceramide species with different fatty‐acid chain lengths play diverse biological functions in various cellular processes, highlighting the importance of ceramide synthases (CerS) in these processes. Migration and cell mobility, a part of these processes, also are effected by ceramide metabolism. However, the molecular mechanism of CerS/ceramide involved is unknown. Here, we investigated the effect of CerS/and ceramide on migration and its related signal pathways in situ and in vivo model. Interestingly, our data show that among CerS only CerS4/ceramide is involved to cell migration and tumor metastasis. Here, we also have generated CerS4−/− mice for in vivo studies. Interestingly, we observed that genetically loss of CerS4 resulted in severe irreversible alopecia, which was associated with hyper‐proliferation and migration of keratinocytes. Mechanistically, we show here that genetic loss or shRNA‐mediated knockdown of CerS4 enhances cell migration by which ligand‐independent signaling of TGF‐beta receptors I and II in various cell types, including keratinocytes, mouse embryonic fibroblasts and cancer cells. Moreover, we found that ceramide directly interact with Smad7 and this interaction was decreased by shRNA‐mediated knockdown of CerS4. Thus, ceramide‐Smad7 binding modulates plasma membrane association of TGF‐βR1 at primary basal cilia, and inhibits its signaling through Sonic‐Hedgehog (Shh) for migration. Furthermore, Ceramide accumulation at the primary basal cilia was decreased by knockdown of CerS4, and this was associated with direct interaction of TGF‐βR1 and SMO receptors in cilia. In fact, inhibition of TGF‐βR /Shh signaling or cilia formation using molecular or pharmacologic inhibitors almost completely prevented cell migration in response to CerS4 knockdown. These data revealed that CerS4/ceramide signaling plays key roles in the regulation of cell migration and metastasis via controlling the TGF‐βR and Shh axis at primary basal cilia.Support or Funding Information1R01 DE016572