Objective Icaritin, one effective metabolite of Herba Epimedii-derived flavonoid icariin, has a strong osteogenic activity. However, its action mechanism remains unclear. Since primary cilia have been shown to play a pivotal role in regulating the osteogenesis, we hypothesized primary cilia are indispensable in mediating icaritin osteogenic effect. Materials and methods Primary rat calvarial osteoblasts were transfected with siRNA1 targeting intraflagellar transport protein 88 (IFT88), a protein required for ciliogenesis, to prevent formation of primary cilium and were treated with 10 −6  M icaritin. Results Alkaline phosphatase (ALP) activity was significantly increased after 3 days in cells transfected with scrambled siRNA control and treated by icaritin (SC+I group) compared to cells transfected with scrambled siRNA control only (SC group). ALP activity after IFT88 siRNA1 transfection and icaritin treatment (siRNA1+I group) was significantly lower than that of SC+I group. Formation of ALP positively stained colonies after 6 days, osteocalcin secretion after 9 days and formation of calcified nodules after 12 days displayed a similar tendency among the three groups. mRNA expression of osteogenesis-related genes ALP, BMP-2, COL1α, RUNX-2 and OSX after 24 h was significantly increased in SC+I group, but was not different with SC group in siRNA1+I group. Protein levels of BMP-2, COL1α, RUNX-2 and OSX after 48 h showed the similar tendency with gene expression. Conclusion Primary cilia are important in mediating icaritin-stimulated osteogenic differentiation and may be a novel target for pharmacological therapies for bone loss.