Neuroimaging and electrophysiological studies provide evidence of hemispheric differences in processing faces and, in particular, emotional expressions. However, the timing of emotion representation in the right and left hemisphere is still unclear. Transcranial magnetic stimulation combined with electroencephalography (TMS-EEG) was used to explore cortical responsiveness during behavioural tasks requiring processing of either identity or expression of faces. Single-pulse TMS was delivered 100 ms after face onset over the medial prefrontal cortex (mPFC) while continuous EEG was recorded using a 60-channel TMS-compatible amplifier; right premotor cortex (rPMC) was also stimulated as control site. The same face stimuli with neutral, happy and fearful expressions were presented in separate blocks and participants were asked to complete either a facial identity or facial emotion matching task. Analyses performed on posterior face specific EEG components revealed that mPFC-TMS reduced the P1–N1 component. In particular, only when an explicit expression processing was required, mPFC-TMS interacted with emotion type in relation to hemispheric side at different timing; the first P1–N1 component was affected in the right hemisphere whereas the later N1–P2 component was modulated in the left hemisphere. These findings support the hypothesis that the frontal cortex exerts an early influence on the occipital cortex during face processing and suggest a different timing of the right and left hemisphere involvement in emotion discrimination.