It is well know that the interaction between poorly damped LC input filter with dc-dc converter lead to degradation of dynamic performance and fault scenario of the system. This problem also often occurs in fuel cell systems. Due to the relatively low and unregulated output voltage, the high gain boost converter is need in such application. A floating interleaved boost converter (FIBC) is selected as a good candidate to achieve this desired effect. In order to ensure the system stability, this paper addresses a method which permits to design a fault-tolerant stabilizing system for the proposed converter and the filter. It consists in implementing an active stabilizer for each switch. Afterward, a method to design fault-tolerant stabilizing system is developed. The simulation results are reported to verify the effectiveness of the proposed method.