This article studies the tracking control of a class of nonlinear systems with input saturation, subject to nonaffine faults and unknown control direction. A fault-tolerant command filtered control (CFC) method based on adaptive neural networks (NNs) is proposed for this kind of nonlinear system. First, the combination of CFC and error compensation overcomes the "explosion of complexity" issue and alleviates the impact of filter errors. Then, a set of radial basis function NNs is constructed to approximate the unknown nonlinear items containing the nonaffine fault function. Additionally, the issue of unknown control direction in the system is effectively resolved by using Nussbaum gain technology. It is proven that the designed controller can ensure that all signals in the closed-loop system are bounded and convergent, and the upper bound of the absolute value of system tracking error is given. Finally, three comparative simulation results are illustrated to show the effectiveness of the proposed method.