This article investigates the stabilization and control problems for a general active fault-tolerant control system (AFTCS) in a stochastic framework. The novelty of the research lies in utilizing uncertain nonhomogeneous Markovian structures to take account for the imperfect fault detection and diagnosis (FDD) algorithms of the AFTCS. The underlying AFTCS is supposed to be modeled by two random processes of Markov type; one characterizing the system fault process and the other describing the FDD process. It is assumed that the FDD algorithm is imperfect and provides inaccurate Markovian parameters for the FDD process. Specifically, it provides uncertain transition rates (TRs); the TRs that lie in an interval without any particular structures. This framework is more consistent with realworld applications to accommodate different types of faults. It is more general than the previously developed AFTCSs because of eliminating the need for an accurate estimation of the fault process. To solve the stabilizability and the controller design problems of this AFTCS, the whole system is viewed as an uncertain nonhomogeneous Markovian jump linear system (NHMJLS) with time-varying and uncertain specifications. Based on the multiple and stochastic Lyapunov function for the NHMJLS, first a sufficient condition is obtained to analyze the system stabilizability and then, the controller gains are synthesized. Unlike the previous fault-tolerant controllers, the proposed robust controller only needs to access the FDD process, besides it is easily obtainable through the existing optimization techniques. It is successfully tested on a practical inverted pendulum controlled by a fault-prone DC motor.