While psychiatry and clinical psychology have long discussed the topic of unconscious emotion, and its potentially explanatory role in psychopathology, this topic has only recently begun to receive attention within cognitive neuroscience. In contrast, neuroscientific research on conscious vs. unconscious processes within perception, memory, decision-making, and cognitive control has seen considerable advances in the last two decades. In this article, we extrapolate from this work, as well as from recent neural models of emotion processing, to outline multiple plausible neuro-cognitive mechanisms that may be able to explain why various aspects of one's own emotional reactions can remain unconscious in specific circumstances. While some of these mechanisms involve top-down or motivated factors, others instead arise due to bottom-up processing deficits. Finally, we discuss potential implications that these different mechanisms may have for therapeutic intervention, as well as how they might be tested in future research.