Our visual inputs are often entangled with affective meanings in natural vision, implying the existence of extensive interaction between visual and emotional processing. However, little is known about the neural mechanism underlying such interaction. This exploratory transcranial magnetic stimulation (TMS) study examined the possible involvement of the early visual cortex (EVC, Area V1/V2/V3) in perceiving facial expressions of different emotional valences. Across three experiments, single-pulse TMS was delivered at different time windows (50–150 msec) after a brief 10-msec onset of face images, and participants reported the visibility and perceived emotional valence of faces. Interestingly, earlier TMS at ∼90 msec only reduced the face visibility irrespective of displayed expressions, but later TMS at ∼120 msec selectively disrupted the recognition of negative facial expressions, indicating the involvement of EVC in the processing of negative expressions at a later time window, possibly beyond the initial processing of fed-forward facial structure information. The observed TMS effect was further modulated by individuals' anxiety level. TMS at ∼110–120 msec disrupted the recognition of anger significantly more for those scoring relatively low in trait anxiety than the high scorers, suggesting that cognitive bias influences the processing of facial expressions in EVC. Taken together, it seems that EVC is involved in structural encoding of (at least) negative facial emotional valence, such as fear and anger, possibly under modulation from higher cortical areas.