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Yoga is effective in binge eating disorder (BED) treatment, but it does not seem effective enough to improve low physical fitness. In contrast, high-intensity interval training (HIIT) is effective in improving physical fitness but has never been studied in the context of BED. In the study, 47 young inactive females with mild to moderate BED were recruited and randomly assigned to a HIIT group (HIIT), a Yoga group (YG), or a control group (CG; age, 19.47 ± 0.74, 19.69 ± 0.874, and 19.44 ± 0.63 years; BMI, 21.07 ± 1.66, 21.95 ± 2.67, and 20.68 ± 2.61 kg/m², respectively). The intervention groups participated in 8-week specific exercises, while the CG maintained their usual daily activity. Before and after the training, participants were evaluated for BED using the binge eating scale (BES) and for physical fitness. The obtained data were compared within groups and between groups, and a correlation analysis between BES and physical fitness parameters was performed. After the training, the YG presented significant improvements in BES (- 20.25%, p = 0.006, η_p² = 0.408), fat mass (FM, - 3.13%, p = 0.033, η_p² = 0.269), and maximal oxygen consumption (VO₂max, 11.51%, p = 0.000, η_p² = 0.601), whereas the HIIT showed significant improvements in body weight (BW, - 1.78%, p = 0.006, η_p² = 0.433), FM (- 3.94%, p = 0.033, η_p² = 0.285), and BMI (- 1.80%, p = 0.006, η_p² = 0.428), but not in BES. Comparisons between groups revealed that both HIIT and YG had significantly higher VO₂max levels than CG (HIIT 12.82%, p = 0.006, η_p² = 0.088; YG: 11.90%, p = 0.009, η_p² = 0.088) with no difference between HIIT and YG. Additionally, YG presented significantly lower BES than both HIIT (15.45%, p = 0.02, η_p² = 0.03) and CG (11.91%, p = 0.022, η_p² = 0.03). In conclusion, Yoga is an effective treatment for BED, but HIIT is not, despite its high efficacy in improving physical fitness.