Academic emotions play an important and complex role in self-regulated learning (SRL). However, few studies have examined how academic emotions unfold in different phases of SRL and how the changes in these emotions influence learning performance. The current study examines 98 students' academic emotion trajectories and profiles across the three phases of SRL (i.e., forethought, performance, and self-reflection) as they solve a clinical problem in BioWorld. Specifically, BioWorld is a simulated learning environment where medical students are tasked with diagnosing virtual patient diseases. We identified the three phases of SRL based on students' problem-solving behaviors and we asked students to self-report their achievement and epistemic emotions at the end of each phase of SRL. The growth curve model results showed that curiosity and confusion declined across the three phases of SRL, whereas boredom increased in the self-reflection phase of SRL. The initial levels of curiosity and enjoyment positively predicted students' performance. Latent transition analysis revealed three emotion profiles: curious-positive, confused-negative, and medium-low. Curious-positive students maintained a relatively stable profile through the SRL phases, whereas students in the confused-negative and medium-low groups exhibited specific transition patterns in their emotions. This study makes theoretical contributions by highlighting the temporal and dynamic nature of emotions in problem-solving. Findings from this study have educational implications regarding the role of specific emotions in learning, the development of one's awareness of their emotions, and emotion regulation.