This paper proposes a method to precisely manipulate a microrobot in the pulsatile flow that simulates the flow characteristics of human blood vessels by utilizing the electromagnetic transfer function of a magnetic navigation system (MNS). The frequency response characteristics of the MNS were utilized so that the input voltages in each coil can precisely generate the required time varying magnetic force of a microrobot. An experiment which successfully anchoring a microrobot in a pulsatile flow was conducted to verify the proposed method.