Past research has provided conflicting evidence concerning whether emotional processing in the amygdala arises independent of selective attention to threat-related stimuli or instead depends on attentional resources and top-down voluntary control. Here, we combine repetitive transcranial magnetic stimulation (rTMS) targeting the right frontal eye field (FEF) with functional magnetic resonance imaging (fMRI) to examine how perturbing top-down attentional control is associated with changes in neural responses to emotional stimuli in visual cortex and amygdala. Participants performed a matching task in which they had to judge whether task-relevant image pairs were similar or different while ignoring task-irrelevant pairs. On each trial, one pair showed houses and the other pair displayed either neutral or fearful faces. The task was performed in two sessions following either rTMS or no TMS, in counterbalanced order. Behavioral results revealed that right FEF perturbation selectively slowed responses to neutral but not fearful faces. ROI analyses revealed selective changes in fusiform face area (FFA) responses to neutral faces following FEF rTMS, while responses to fearful faces were relatively preserved; in parallel, amygdala responses to fearful faces remained intact or showed increased activation. A control group undergoing the same protocol with rTMS applied to the vertex (VTX) showed no significant changes in behavioral performance or neural activation patterns. Together, these findings suggest that neural responses to emotionally salient stimuli may be less dependent on top-down attentional modulation than responses to neutral stimuli, consistent with models proposing partially distinct contributions of attentional and emotional processing networks.