Brain stimulation technologies have seen increasing application in basic science investigations, specifically toward the goal of improving memory function. However, proposals concerning the neural mechanisms underlying cognitive enhancement often rely on simplified notions of excitation. As a result, most applications examining the effects of transcranial magnetic stimulation (TMS) on functional neuroimaging measures have been limited to univariate analyses of brain activity. We present here analyses using representational similarity analysis (RSA) and encoding-retrieval similarity (ERS) analysis to quantify the effect of TMS on memory representations. To test whether an increase in local excitability in PFC can have measurable influences on upstream representations in earlier temporal memory regions, we compared 1 and 5Hz stimulation to the left dorsolateral PFC (DLPFC). We found that 5Hz rTMS, relative to 1Hz, had multiple effects on neural representations: 1) greater representational similarity during both encoding and retrieval in ventral stream regions, 2) greater ERS in the hippocampus, and, critically, 3) increasing ERS in MTL was correlated with increasing univariate activity in DLPFC, and greater functional connectivity for hits than misses between these regions. These results provide the first evidence of rTMS modulating semantic representations and strengthen the idea that rTMS may affect the reinstatement of previously experienced events in upstream regions.