Emotion modulates our time perception. So far, the relationship between emotion and time perception has been examined with visible emotional stimuli. The present study investigated whether invisible emotional stimuli affected time perception. Using continuous flash suppression, which is a kind of dynamic interocular masking, supra-threshold emotional pictures were masked or unmasked depending on whether the retinal position of continuous flashes on one eye was consistent with that of the pictures on the other eye. Observers were asked to reproduce the perceived duration of a frame stimulus that was concurrently presented with a masked or unmasked emotional picture. As a result, negative emotional stimuli elongated the perceived duration of the frame stimulus in comparison with positive and neutral emotional stimuli, regardless of the visibility of emotional pictures. These results suggest that negative emotion unconsciously accelerates an internal clock, altering time perception.