A robust neural network controller (NNC) is presented for tracking control of underwater vehicles with uncertainties. The controller is obtained by using backstepping technique and Lyapunov function design in combination with neural network identification. Modeling errors and environmental disturbances are considered in the mathematical model. A two-layer neural network is introduced to compensate the modeling errors, while H∞ control strategy is used to achieve the L2-gain performance. The uniformly ultimately bounded (UUB) stabilities of tracking errors and NN weights are guaranteed through the proposed controller. An on-line NN weights tuning algorithm is also proposed. Good performances of the tracking control system are illustrated by the results of numerical simulations.