Individuals exhibit a time orientation, known as a chronotype, which is the latest (i.e., becoming an evening-type ET) in their 20 s, such as university students. In a morning-oriented society, the sleep patterns of individuals with ET are affected, which can lead to health problems. Particularly in the age of mobile devices, ET students seem to use their mobile devices more often (especially before going to bed), which leads to sleep problems. We aimed to investigate the association between body composition problems and chronotypes in females. The study assessed the physical activity levels (PAL), dietary status, Morningness-Eveningness Questionnaire (MEQ) scores, and body composition of 251 students. Subsequently, 195 students with a body mass index (BMI) within the normal range (18.5–24.9 kg/m2) were included in the analysis. Multiple regression analyses showed that the percentage of body fat (BF) was significantly negatively associated with the MEQ and PAL. Forty-nine of the participants were in the ET group (MEQ ≤ 41) and 47 in the non-ET group (MEQ ≥ 54 = mean + S.D. / 1.5), and participants with higher BF (≥30%) were more likely to be in the ET group (43% vs. 21%, P < 0.05). Such state of high BF despite a normal BMI is defined as normal-weight obesity. Therefore, young females (especially ET individuals) may be required to take chronotype-specific measures to help them maintain an appropriate body composition, such as the use of ergonomic devices.