In this work, the synthesis of fault tolerant control (FTC) for stochastic stability and H-infinity performance is studied. Occurrence of faults in the system is governed by a Markov Chain, so the open-loop system is modelled as a linear system with Markovian jumping parameters. The fault detection and isolation (FDI) decision is modelled as another random process that will indicate the fault mode after an exponentially distributed random delay. This stochastic formulation of FTC concerns the random nature of faults and the effect of random fault detection delay on the overall system, and can be regarded as an extension to the traditional reconfigurable control problem. In this paper, output feedback controllers are designed using an iterative LMI algorithm for mean exponential stability (MES) and the H-infinity performance. Model uncertainties and external disturbance are also considered in the robust design.