This paper presents on-demand microbeads delivery system in a microfluidic chip by magnetically driven microtool (MMT). The four of horizontally arranged permanent magnets and the piezoelectric vibrator are used to actuate the Ni based microtool precisely in the chip. The MMT injects the beads mechanically to flow and then into ejection operation part. We succeeded in transferring microbeads one by one with the required pace to the next process in order to achieve stable dispensing microbeads out from the microfluidic chip to incubation environment. We succeeded in demonstration of the delivery and ejection of polystyrene beads (100 m) with the flow velocity of from 0.02 ml/h to 0.04 ml/h and MMT frequency from 1 Hz to 6 Hz to adjust the pitch of each micro-bead. The spacing interval of microbeads could be mainly adjusted by changing of MMT frequency and the flow velocity of output stream. The proposed system shows advantages of high-speed, high success ratio and disposable of microfluidic chip having MMT.