This research examined learning-related achievement emotions that are experienced in the context of preparing a master’s thesis. These emotions are defined within the control-value theory of achievement emotions (Pekrun, 2006) as affective experiences that are experienced during academic learning activities in which achievement is possible. Their occurrence depends on cognitive determinants, i.e., control and value appraisals. In this research were examined positive - enjoyment, hope, and pride, and negative emotions - anger, anxiety, shame, helplessness, and boredom. The process of preparing a master’s thesis is characterized by various emotions, but also by uncertainty. Intolerance of uncertainty is closely related to dealing with uncertainty and is defined as a cognitive bias that affects perception, interpretation, and response to uncertain situations. Intolerance of uncertainty could play an important role in the experience of emotions; therefore, the aim of this study was to test the moderating effect of intolerance of uncertainty in the relationship between control and value appraisals and achievement emotions in the context of preparing a master’s thesis. The study involved 258 graduate students who completed an online survey questionnaire. The results suggest that cognitive determinants positively predict the experience of positive and negatively predict the experience of negative emotions related to learning. In addition, a positive contribution of intolerance of uncertainty was found for all negative emotions. The moderating effect of intolerance of uncertainty in the relationship between cognitive determinants and achievement emotions was insignificant for all emotions except anxiety. Specifically, a weakening of the negative effect of cognitive determinants on anxiety was observed, which was more pronounced at higher levels of intolerance of uncertainty.