Unconscious processes are often assumed immune from attention influence. Recent behavioral studies suggest however that the processing of subliminal information can be influenced by temporal attention. To examine the neural mechanisms underlying these effects, we used a stringent masking paradigm together with fMRI to investigate how temporal attention modulates the processing of unseen (masked) faces. Participants performed a gender decision task on a visible neutral target face, preceded by a masked prime face that could vary in gender (same or different than target) and emotion expression (neutral or fearful). We manipulated temporal attention by instructing participants to expect targets to appear either early or late during the stimulus sequence. Orienting temporal attention to subliminal primes influenced response priming by masked faces, even when gender was incongruent. In addition, gender-congruent primes facilitated responses regardless of attention while gender-incongruent primes reduced accuracy when attended. Emotion produced no differential effects. At the neural level, incongruent and temporally unexpected primes increased brain response in regions of the fronto-parietal attention network, reflecting greater recruitment of executive control and reorienting processes. Congruent and expected primes produced higher activations in fusiform cortex, presumably reflecting facilitation of perceptual processing. These results indicate that temporal attention can influence subliminal processing of face features, and thus facilitate information integration according to task-relevance regardless of conscious awareness. They also suggest that task-congruent information between prime and target may facilitate response priming even when temporal attention is not selectively oriented to the prime onset time.