In this paper, an adaptive neural network controller is proposed for vibration suppression of a multisectional riser system with unknown boundary disturbance, time‐varying asymmetric output constraint, and input nonlinearity. The considered riser system is composed of a continuous connection of several different pipes, and its dynamic models are represented by a set of multiple continuously connected partial differential equations (PDEs) and an ordinary differential equation (ODE) at the top boundary. Considering input nonlinearity, external disturbance, and system uncertainty, radial basis function (RBF) neural networks are adopted to eliminate the effect of these uncertain terms. Besides, a barrier Lyapunov function is employed to guarantee the restrictions. With the proposed boundary control, the stability of the closed‐loop system is proved and simulations are given to illustrate the well performance of the proposed control strategy.