We propose a new and feasible scheme to implement quantum gates in decoherence-free subspaces (DFSs) with Josephson charge qubits situated in a circuit QED architecture. Based on the resonator-assisted interaction, the controllable interqubit couplings occur only by tuning the individual flux biases, by which we obtain the DFS-encoded universal quantum gates. Compared with the non-DFS situation, we numerically consider the robustness of the DFS-encoded scheme that can be insensitive to the collective noises. Thus the protocol may perform the fault-tolerant quantum computing with Josephson charge qubits.