The recognition of facial expressions of emotion is crucial for social interactions. Previous neuroimaging and brain stimulation studies have suggested the involvement of the prefrontal cortex (PFC) in the regulation of emotions. Upon this background, in this study we directly examined the specific impact of prefrontal regulation on the recognition of facial emotions using transcranial magnetic stimulation (TMS). Our results showed that inhibition of the dorsal lateral prefrontal cortex (dlPFC) through continuous theta-burst stimulation (cTBS) significantly enhanced individuals’ ability to regulate emotional biases when recognizing ambiguous facial expressions that morphed between prototypical neutral and emotional faces. Conversely, the intermittent theta-burst stimulation (iTBS) protocol yielded no discernible effects. These findings provide direct evidence supporting that inhibiting prefrontal responses can facilitate the regulation required to mitigate emotional biases.