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While academic emotions play a complex role in self-regulated learning (SRL), few studies have examined how academic emotions unfold in different phases of SRL and how the change of these emotions influence learning performance. This study examines 129 medical students’ academic emotion trajectories across different phases of SRL as they solve a clinical problem in a simulated learning environment. The growth curve model findings revealed that curiosity and confusion declined across the three phases of SRL, whereas boredom increased in the self-reflection phase of SRL. The initial level of curiosity and enjoyment positively predict students’ final performance. These findings highlight the temporal nature of emotions in SRL and provide insights that can lead to implications for instruction.