Abstract Background Chronotype is a sleep-wake cycle that reflects individuals’ daily activity patterns. It has been suggested that evening-type individuals have increased risk of adverse outcomes. However, chronotype also relates to their innate characteristics. The purpose of this study was to investigate whether those characteristics mediate the relationships of chronotype with physical and mental outcomes. Methods A total of 146 Japanese university students participated in a web survey in October 2022. The data of 131 respondents (44 males and 87 females: aged from 18 to 27 years) were eligible for analysis. The following information was assessed: 1) Munich Chrono Type Questionnaire (MCTQ: Roenneberg et al., 2003), 2) Body mass index (BMI: calculated from self-report height and weight), and 3) Cognitive reflection test (CRT: Frederick, 2005). We hypothesized that BMI would be higher in evening-type students compared to morning-type students. We also hypothesized that subjects’ CRT score would be better when they took the test at a proper action time, i.e., a time that is matched to their own chronotype. Results The percentage of students in morning-type was significantly higher for females (49.4 %) than males (31.8 %). Analysis of variance (ANOVA) indicated that morning-type males had significantly higher BMI compared to evening-type males. On the other hand, morning-type females had significantly lower BMI compared to evening-type females. Another ANOVA indicated that males who took the CRT at the time matched to their chronotype had significantly less errors. Such a difference, however, was not found in females. Conclusions As predicted, while chronotype was associated with BMI and CRT score, the relationships were moderated by gender and the task execution time. The implication of the study was that researchers would be required to consider those moderating factors when investigating the effect of chronotype on physical and mental health. Key messages • A web survey was conducted for 146 Japanese university students to examine the relationships of chronotype with body mass index and cognitive performance. • The analysis indicated that gender and the task execution time moderate the effect of chronotype on physical and mental health.