ABSTRACT Many studies have reported poor school achievement in evening persons and general circadian fluctuations in cognition. The aim of this study was to analyze circadian fluctuations in a cross-sectional design and examine the effects of chronotype on situational emotions and intrinsic motivation. A cross-sectional survey study was conducted in three Turkish secondary schools with a total sample of 599 students (283 females and 316 males). Data were collected at the end of specific math lessons of the same grade level and content, using a form combining three scales. We found no gender-related differences in intrinsic motivation, while there were some differences in situational motivation. In math classes, female students exhibited higher level of interest, while boys scored higher on boredom. In addition, students who scored high on morning affect reported higher levels of interest, well-being, and less boredom. Students with higher stability (and lower fluctuations in mood and cognition during the day) reported a higher degree of enjoyment, perceived competence, perceived choice, and less pressure/tension in their math lessons. A positive association was observed between distinctness, interest, and well-being, while negative correlations existed between distinctness and boredom. This suggests that students with higher diurnal stability reported a higher level of interest, well-being, and a lower level of boredom. Additionally, the results of the analyses showed that morningness, distinctness, and eveningness were significant predictors of intrinsic motivation. Conversely, gender, time of application, morningness, and distinctness emerged as predictors for situational emotions in mathematics classes.