The strong coupling of quantum emitters to a cavity mode has been of paramount importance in the development of quantum optics. Recently, also the strong coupling to more than a single mode of an electromagnetic resonator has drawn considerable interest. We investigate how this multimode strong coupling regime can be harnessed to coherently control quantum systems at the single-photon level. Specifically, we demonstrate that a Maxwell-Fish-Eye lens can be used to implement a pulsed excitation-exchange between two distant quantum emitters. This periodic exchange is mediated by single-photon pulses and can be extended to a photon-exchange between two atomic ensembles, for which the coupling strength is enhanced collectively.