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Small group learning activities have been shown to improve student academic performance and educational outcomes. Yet, we have an imperfect understanding of the mechanisms by which this occurs. Group learning may mediate student stress by placing learning in a context where students have both social support and greater control over their learning. We hypothesize that one of the methods by which small group activities improve learning is by mitigating student stress. To test this, we collected physiological measures of stress and self-reported perceived stress from 26 students in two undergraduate classes. Salivary cortisol and testosterone were measured within students across five contexts: a) pre-instructional baseline, b) following a traditional lecture, c) after participating in a structured small group learning activity, d) following completion of multiple choice, and e) essay sections of an exam. Results indicate students have lower salivary cortisol after small group learning activities, as compared to traditional lectures. Further, there is no evidence of a relationship between physiological measures of stress and self-reported perceived stress levels. We discuss how structured small group activities may be beneficial for reducing stress and improving student learning outcomes.