Background Medical students experience high levels of stress during training due to demanding course loads which often leaves less time for self-care. This study combines the self-care technique of yoga with learning anatomical locations, innervations, actions, and functions of the muscles and organs to determine if anatomy tests scores are improved and whether students’ stress levels attenuate from participating in yoga. Methods In this randomized controlled study, 64 student volunteers were randomized into either a yoga intervention group or wait list control group throughout the M1 anatomy course. The yoga group (n = 32) participated in 8 yoga sessions synced with the anatomy topics they were learning in lecture. The wait list group (n = 32) went through their normal anatomy curriculum but had an option to participate in the same yoga sessions after the anatomy course. The primary research purpose was to determine whether yoga improved anatomy exam performance by comparing four anatomy exam scores between the two groups. The secondary research purposes included the following: to determine whether yoga classes including anatomy teaching still conferred acute and long-lasting stress relief by, respectively, comparing a students’ own pre- and post-yoga stress level and self-perceived stress levels between the two groups; and to determine if a student’s confidence in anatomy was improved after a yoga session. Results There was no significant difference in anatomy exam performance between students who received yoga and those on the waitlist (all p > 0.05). For students who received yoga, their average self-reported stress levels decreased after each yoga session, their average DASS (Depression, Anxiety and Stress Scale) score decreased after a yoga session, but they were not significantly less stressed than their waitlist peers prior to an exam, and their self-reported confidence in anatomy material related to the back, upper extremity, head and neck, and abdomen/pelvis increased. Conclusion With this sample, there was no evidence that yoga sessions paired with anatomy lecture material improved overall anatomy exam performance, as opposed to only the musculoskeletal portion which other studies have looked at. However, yoga acutely reduced stress levels, and subjective feelings of knowledge improvement were noted by participants. Both of these can provide benefits to medical students.