Despite the importance of emotion regulation in education there is a paucity of research examining it in authentic educational contexts. Moreover, emotion measurement continues to be dominated by self-report measures. We address these gaps in the literature by measuring emotion regulation and activation in 37 medical students’ who were solving medical cases using BioWorld, a computer based learning environment. Specifically, we examined students’ habitual use of emotion regulation strategies as well as electrodermal activation (emotional arousal) from skin conductance level (SCL) or skin conductance response (SCR), as well as appraisals of control and value and self-reported emotional responses during a diagnostic reasoning task in Bioworld. Our results revealed that medical students reported significantly higher habitual levels of reappraisal than suppression ER strategies. Higher habitual levels of reappraisal significantly and positively predicted learners’ self-reported pride. On the other hand, higher habitual levels of suppression significantly and positively predicted learners’ self-reported anxiety, shame, and hopelessness. Results also revealed that medical students experienced relatively low SCLs and few SCRs while interacting with Bioworld. Habitual suppression strategies significantly and positively predicted medical students’ SCLs, while SCRs significantly and positively predicted their diagnostic efficiency. Findings also revealed a significant, positive predictive relationship between SCL and shame and anxiety and the inverse relationship between SCL and task value. Implications and future directions are discussed.