This paper addresses the problem of adaptive tracking control for a class of stochastic nonlinear systems with time-varying input delays, and the nonlinear functions of the systems are with not only the unknown parameters but also the unknown state time-varying delays, which is different from the previous work. In this paper, through a state transformation, the system can be easily transformed into a system without the time-varying input delay; the appropriate Lyapunov–Krasovskii functionals are used to compensate the unknown time-varying delay terms, and the quadratic functions instead of the quartic functions often utilized in the existing results are used as Lyapunov functions to analyze the stability of systems and the hyperbolic tangent functions are introduced to deal with the Hessian terms. Fuzzy logic systems (FLSs) in Mamdani type are used to approximate the unknown nonlinear functions. Then, based on the backstepping technique, the adaptive fuzzy controller is designed. The three main advantages of the developed scheme are that (i) unlike the existing results which deal with the nonlinearly parameterized functions by using the separation principle, the nonlinearly parameterized functions are lumped into the continuous functions which can be approximated by using the FLS; (ii) the number of the adjusted parameters only depend on the order of the investigated systems, which can reduce the computational burden greatly; and (iii) the existence of the time-varying input delay such that the controller design becomes much more difficult, and in this paper, it can be dealt with by using an appropriate state transformation. It is proven that all the signals of the closed-loop system are semi-globally uniformly ultimately bounded in probability, whereas the tracking error converges to a small neighborhood of the origin. Finally, simulation results are provided to show the effectiveness of the proposed approach.