The invention provides systems and methods enabling high fidelity quantum communication over long communication channels even in the presence of significant loss in the channels. The invention involves laser manipulation of quantum correlated atomic ensembles using linear optic components (110, 120), optical sources of low intensity pulses (10), interferers in the form of beam splitters (150), and single-photon detectors (180, 190) requiring only moderate efficiencies. The invention provides fault-tolerant entanglement generation and connection using a sequence of steps that each provide built-in entanglement purification and that are each resilient to realistic noise levels. The invention relies upon collective rather single particle excitations in atomic ensembles and results in communication efficiency scaling polynomially with the total length of the communication channel.