Background: Biomarkers for psychological stress have been examined and the “gut–microbiota–brain axis” is currently attracting attention. An intervention study reported improvements in both the intestinal environment and psychological stress. However, the relationship between psychological stress scores and urinary 5-hydroxytryptamine (u-5-HT), produced by enterochromaffin cells in the intestinal tract, has not yet been investigated over time in healthy subjects under psychological stress. Therefore, the present study examined the relationship between subjective psychological stress (depression and anxiety) scores and u-5-HT levels over time in healthy women. Methods: The effects of the objective structured clinical examination (OSCE), considered to be a uniform source of psychological stress, on u-5-HT levels were assessed in 16 third-year female medical university students (21.3 ± 2.1 years old) in Japan with a normal menstrual cycle. A self-administered questionnaire consisting of Zung’s Self-rating Depression Scale (SDS) and State-Trait Anxiety Inventory (STAI) was used to evaluate subjective stress 1 month, 1 week, and 1 day before and 1 week after the OSCE. Pearson’s product-momentum correlation coefficient was used to calculate the correlation coefficient between u-5-HT levels, STAI, and SDS for each examined period. Result: On the day before the OSCE, u-5-HT levels correlated with SDS and STAI (SDS: r = .524, P = .037, State-Anxiety: r = −.718, P = .002). Conclusion: A correlation was observed between subjective psychological stress scores and u-5-HT levels in healthy women under psychological stress.