Robustness and reliability are two key requirements for developing practical quantum control systems. The purpose of this article is to design a coherent feedback controller for a class of linear quantum systems suffering from Markovian jumping faults so that the closed-loop quantum system has both fault tolerance and H^infty disturbance attenuation performance. This article first extends the physical realization conditions from the time-invariant case to the time-varying case for linear stochastic quantum systems. By relating the fault-tolerant H^infty control problem to the dissipation properties and the solutions of Riccati differential equations, an H^infty controller for the quantum system is then designed by solving a set of linear matrix inequalities. In particular, an algorithm is employed to introduce additional quantum inputs and to construct the corresponding input matrices to ensure the physical realizability of the quantum controller. Also, we propose a real application of the developed fault-tolerant control strategy to quantum optical systems. A linear quantum system example from quantum optics, where the amplitude of the pumping field randomly jumps among different values due to the fault processes, can be modeled as a linear Markovian jumping system. It is demonstrated that a quantum H^infty controller can be designed and implemented using some basic optical components to achieve the desired control goal for this class of systems.