A large part of research using questionnaires for female university students relies on self-reported body mass, height, and body mass index (BMI) data; however, the validity of these data in this population group is unknown. Therefore, the aim of the present study is to examine the validity of self-reported body mass, height, and BMI in female students. Female students of biomedical sciences (n = 93, age 21.8 ± 4.7 years, height 1.63 ± 0.06 m, weight 60.5 ± 11.9 kg, and BMI 22.7 ± 3.8 kg/m2) completed the short version of the International Physical Activity Questionnaire and were tested for anthropometric characteristics at three different times of the day (12–2 p.m., n = 36; 2–4 p.m., n = 20; 4–6 p.m., n = 37). Participants over-reported height (+0.01 ± 0.02 m, +0.9 ± 1.2%, Cohen’s d = 0.22) and under-reported weight (−0.8 ± 2.1 kg, −1.2 ± 3.6%, d = −0.07) and BMI (−0.7 ± 1.0 kg/m2, −2.9 ± 4.2%, d = −0.19) (p < 0.001). A moderate main effect of time of day on %Δweight (p = 0.017, η2 = 0.086) and %ΔBMI (p = 0.045, η2 = 0.067), but not on %Δheight (p = 0.952, η2 = 0.001), was observed, where the group tested at 4–6 p.m. under-reported weight and BMI more than the 2–4 p.m. group. The weekly metabolic equivalent (MET) × min did not correlate with %Δheight (r = 0.06, p = 0.657), but its correlations with %Δweight (r = −0.27, p = 0.051) and %ΔBMI (r = −0.238, p = 0.089) reached statistical significance. Participants in the early follicular phase reported BMI more accurately (p = 0.084, d = 0.68) than those in the mid-luteal phase. In conclusion, female students over-reported height and under-reported weight and BMI. Under-reporting weight and BMI is influenced by time of day and menstrual cycle phase. These findings should be considered by health professionals and researchers when administering questionnaires to female students.