This paper considers a consensus problem of leader-following multiagent system with unknown dynamics and jointly connected topologies. The multiagent system includes a self-active leader with an unknown acceleration and a group of autonomous followers with unknown time-varying disturbances; the network topology associated with the multiagent system is time varying and not strongly connected during each time interval. By using linearly parameterized models to describe the unknown dynamics of the leader and all followers, we propose a decentralized adaptive tracking control protocol by using only the relative position measurements and analyze the stability of the tracking error and convergence of the adaptive parameter estimators with the help of Lyapunov theory. Finally, some simulation results are presented to demonstrate the proposed adaptive tracking control.