This paper studies the leader-following consensus of second-order multi-agent systems with input delays. Firstly, a feedback-tracking control protocol with the leader’s delayed state derivative is proposed to guarantee the leader-following consensus. Secondly, considering the same input delay of the second-order multi-agent system, the explicit formula of the upper bound of delay for the asymptotic stability of the second-order multi-agent system is obtained by using the frequency domain analysis method. Compared with the latest existing controllers, the controller designed in this paper improves the convergence speed and tracking accuracy. Thirdly, a variety of diverse input delays are further considered, the feedback tracking controller is designed to improve the convergence speed and tracking accuracy, and sufficient conditions of leader-following consensus are given by using the generalized Nyquist stability criterion. Finally, simulation examples are given to show the effectiveness of our control protocol.