Objective Most previous studies have concluded that decreased cognitive function and performance due to ultra-short acting hypnotics do not persist after 6–9 h post-administration. This study examined the effects of ultra-short acting hypnotics on cognitive function and performance 12 h after administration, ie, a time considered sufficient for the effects of hypnotics to disappear. Methods Thirteen healthy young male volunteers (mean age, 23.4 ± 3.2 years) participated in this study. Participants attended three sessions of polysomnography (PSG) recording preceded by oral administration of placebo for the first session, and 5 mg zolpidem or 0.25 mg triazolam for the second and third sessions, in a double-blinded, randomized manner at intervals of at least five days. A cognitive test battery was administered following each session, consisting of a psychomotor vigilance task (PVT), which reflects alertness and sleepiness, digit symbol substitution test (DSST), which reflects attention and working memory function, and assessment of subjective sleepiness and mental condition using a visual analog scale (VAS). Results and Conclusions The administration of hypnotics significantly increased total sleep time, sleep efficiency, and sleep stages 2 and 4, and significantly decreased wake after sleep onset and sleep stage 1. PVT parameters were not affected by the administration of hypnotics, but DSST score was significantly lower, and “subjective alertness,” “vigor,” and “sadness” significantly deteriorated, after administration. In conclusion, while objective sleepiness disappeared 12 h after the administration of ultra-short acting hypnotics, their effects to decrease cognitive function persisted even after 12 h post-administration.