Due to irregular daytime routines, chronotype changes, side jobs and exam periods after the COVID-19 pandemic, university students are trying to find new balances in their everyday life. The aim of the present study is to analyze the impact of daytime chronotype and hour preferences for the circadian rhythm on academic achievement among university students, considering their sleep habits and class frequencies in daytime and nighttime classes. Furthermore, this study aimed to analyze the differences in chronotype preferences with regard to age, sex, and academic schedule students are attending. A sample of 87 university second-year Psychology and Management students attending the academic year 2021/2022 after the governmental relief measures of the COVID-19 pandemic completed a 13-item questionnaire on sleep habits and preferences. Further variables encompassed sleep behaviors, such as age, sex, daytime and nighttime classes, as well as academic achievement. The results of the study showed that university students had a higher preference for the morningness type. Additionally, chronotype traits explained 30% (values from regression analysis) of academic achievement but did not directly impact academic results. The sleep-wake cycle diverged among age groups because the youngest participants (19–21 years old) and older participants (35–44 years old) reported higher academic scores during the first semester and the full academic year. No significant differences were identified with respect to sex. There is a lack of literature explaining the effect of sleep hours on academic achievement among students after stay-at-home rules during the COVID-19 pandemic. Thus, it is imperative to understand the difficulties students face with regard to their studying hours, working shifts, and daytime or nighttime classes to create a sustainable university system that attends to students’ needs and necessities.