of an organic molecule embedded inside an optical waveguide and electrically coupled to a superconducting qubit far from the optical axis. We show that high fidelity, photon-mediated, entanglement between distant superconducting qubits can be achieved with incident pulses at the single photon level. Such low light level is highly sought for to overcome the decoherence of the superconducting qubit caused by absorption of optical photons.