To investigate the daily fluctuations in brain temperature in healthy individuals using magnetic resonance (MR) diffusion-weighted imaging (DWI) thermometry and to clarify the associations between the brain and body temperatures and sex. Thirty-two age-matched healthy male and female volunteers (male = 16, 20-38 years) were recruited between July 2021 and January 2022. Brain MR examinations were performed in the morning and evening phases on the same day to calculate the brain temperatures using DWI thermometry. Body temperature was also measured in each MR examination. Group comparisons of body and brain temperatures between the two phases were performed using paired t-tests. A multiple linear regression model was used to predict the morning brain temperature using sex, evening brain temperature, and the interaction between sex and evening brain temperature as covariates. Body temperatures were significantly higher in the evening than in the morning in all participants, male group, and female group (p < 0.001, = 0001, and < 0.001, respectively). Meanwhile, no significant difference was observed between the morning and evening brain temperatures in each analysis (p = 0.23, 0.70, and 0.16, respectively). Multiple linear regression analysis showed significant associations of morning brain temperature with sex (p = 0.038), evening brain temperature (p < 0.001), and the interaction between sex and evening brain temperature (p = 0.036). Unlike body temperature, brain temperature showed no significant daily fluctuations; however, daily fluctuations in brain temperature may vary depending on sex.