The university experience promotes changes in the lives of emerging adults, among which greater use of media, whose proximity to the beginning of sleep causes irregularities in hours and sleep deprivation affecting basic cognitive processes that regulate performance, such as attention, working memory, inhibitory control, and cognitive flexibility. However, performance and sleepiness can suffer a compensatory effect from brain areas that can be reflected in cortical activation and autonomic activity. In this work, we assessed the impact of nighttime cell phone use on sleep irregularities and quality, social jet-lag, daytime sleepiness, and cognitive performance. In parallel, the compensatory effect of the autonomic nervous system to sleep deprivation was assessed through heart rate variability (HRV). 59 students (44 women) from higher education courses in the field of biosciences completed the questionnaire "Health and sleep" and the Epworth Sleepiness Scale. Then, they filled in the sleep diary, where they recorded their cell phone use after 6 pm, and used actimeters for 10 days. In this phase, they performed cognitive tests and collected variables of autonomic response once between 7 and 9 am. A GLM analysis was performed to see the effect of cell phone use after 6 pm on the other variables and 3 structural equation models to see the multiple prediction relationships between the study variables. In general, students slept and woke up earlier, with greater sleepiness on waking in the week and prevalence of excessive daytime sleepiness in the sample. The greater use of cell phones predicted greater daytime sleepiness (β = 0.016; p = 0.03) and HRV (β = 0.460; p = 0.001), as well as less sustained attention (β = 0.115; p = 0.063) and cognitive flexibility (β = -0.064; p = 0.008). The indirect impact of cell phone use after 6 pm on cognition was assessed using structural equation analysis, considering its action via sleep quality and irregularity, as well as changes in HRV and EEG. However, no indirect effects of cell phone use on cognitive variables were found. Therefore, cell phone use after 6 pm was associated with an increase in daytime sleepiness with negative impacts on sustained attention and cognitive flexibility in the morning in university students. Also, cell phone use was associated with increased HRV, which may be related to a compensatory effect of the parasympathetic nervous system to sleep deprivation.