In this study, the dynamics of primary cilium (PC) in a pulsatile blood flow is numerically studied. The two-way fluid-cilium interaction is handled by an explicit immersed boundary-lattice Boltzmann method with the cilium base being modeled as a nonlinear rotational spring (Resnick in Biophys J 109:18–25, 2015 ). The fluid-cilium interaction system is investigated at several pulsatile flow cases, which are obtained by varying the flow peak Reynolds numbers (Repeak ) and Womersley numbers (Wo ). The cilium’s dynamics is observed to be closely related to the Repeak and Wo. Increasing the Repeak or decreasing the Wo results in an increase in cilium’s flapping amplitude, tip angular speed and maximum tensile stress. We also demonstrated that by reducing the Repeak or enhancing the Wo, one can shift the two-side flapping pattern of PC to a one-side one, making the stretch only occurs on one side. During the flapping process, the location of the maximum tensile stress is not always found at the basal region, instead, it is able to propagate from time to time within a certain distance to the base.