This paper demonstrates switching of a single signal photon by a single gating photon of a different frequency, via a cross-phase-modulation. This effect is mediated by materials exhibiting electromagnetically induced transparency (EIT), which are embedded in photonic crystals (PhCs). An analytical model based on waveguide-cavity QED is constructed for our system, which consists of a PhC waveguide and a PhC microcavity containing a four-level EIT atom. It is solved exactly and analyzed using experimentally accessible parameters. It is found that the strong coupling regime is required for lossless two-photon quantum entanglement.