Background: There is evidence of yoga and aerobic exercises as an effective therapy for nurse burnout; however, these methods have yet to be compared. Objectives: This study aimed to compare the effects of yoga and aerobic exercises on burnout among nurses. Methods: This was a randomized controlled trial with a pre-test and post-test design. The study was conducted in two medical and educational hospitals in the south of Iran (February 2019 to April 2019). A total of 81 female nurses were randomized to yoga (n = 27), aerobics (n = 27), and control (n = 27) groups. In this study, 24 sessions of yoga and aerobic practices were run. The Maslach Burnout Inventory was filled out before the intervention, immediately after, and one month later. The data were analyzed using IBM SPSS software 16.0. Shapiro test, analysis of variance (ANOVA) test, chi-square test, Friedman test, and Kruskal-Wallis one-way analysis test were used to analyze the data. Results: A total of 71 participants remained and continued the study, and 56% were married. The participants’ mean age and mean work history were 35.78 ± 3.94 and 11.65 ± 5.10 years, respectively. The mean of overtime work in the month was 35.67 ± 23.85 hours. There were no significant differences between the three groups before intervention (T0) and one month after intervention (T2), although the mean scores of the aerobic and yoga groups were reduced, compared to the control group. Immediately after intervention (T1), a significant difference was observed in emotional exhaustion (P = 0.007, Df = 2, Kruskal-Wallis x2 = 10.016, size effect = 0.95 - 2.26). The mean score of emotional exhaustion in the yoga group (23.13 ± 4.13) was reduced compared to the aerobic (36.00 ± 5.65) and control (38.44 ± 10.96) groups. Conclusions: Both yoga and aerobics reduced burnout, compared to the control group. Yoga was better than aerobics in the emotional exhaustion dimension. Although further research is needed to compare these two interventions, using each of them can reduce the burnout of nurses. Nursing managers can use yoga as an effective method to reduce job burnout. For future research, it is suggested to use other yoga techniques with longer intervention time and long-term follow-up.