In this paper, we investigate the consensus tracking problem of nonlinear MASs with nonuniform time-varying input delays and external disturbances. For each follower, the composited disturbance observer and the state observer are employed to estimate bounded composited disturbances and unmeasured states, and a distributed observer based on output-feedback is proposed to approximate the leader’s states approachably. Sequentially, the consensus tracking control is converted into a stability control problem for the nonlinear MASs with nonuniform time-varying input delays. Subsequently, a distributed controller based on the truncated prediction approach is presented, which only depends on the boundary value of time-varying input delays. The distributed controller can render each follower synchronically stable via the Lyapunov stability theory. Finally, a group of single-link manipulators is used as an example to verify the effectiveness of the theoretical results.