Voxel-wise meta-analyses of task-evoked regional activity were conducted for healthy individuals during the unconscious processing of emotional and neutral faces with an aim to examine whether and how different experimental paradigms influenced brain activation patterns. Studies were categorized into sensory and attentional unawareness paradigms. Thirty-four fMRI studies including 883 healthy participants were identified. Across experimental paradigms, unaware emotional faces elicited stronger activation of the limbic system, striatum, inferior frontal gyrus, insula and the temporal lobe, compared to unaware neutral faces. Crucially, in attentional unawareness paradigms, unattended emotional faces elicited a right-lateralized increased activation (i.e., right amygdala, right temporal pole), suggesting a right hemisphere dominance for processing emotional faces during inattention. By contrast, in sensory unawareness paradigms, unseen emotional faces elicited increased activation of the left striatum, the left amygdala and the right middle temporal gyrus. Additionally, across paradigms, unconsciously processed positive emotions were found associated with more activation in temporal and parietal cortices whereas unconsciously processed negative emotions elicited stronger activation in subcortical regions, compared to neutral faces.