Introduction: Breast cancer and its treatments lead to several physical and psychological repercussions in the short and long term. Furthermore, breast cancer survivors (BCS) tend to present sedentary behavior, which worsens the aforementioned breast cancer treatment side effects. Physical exercise has been demonstrated to be effective for improving physical and psychological BCS aspects. Therefore, the purpose of this study is to investigate the effects of 24 weeks of supervised Mat Pilates on force production, flexibility, postural control, gait, body composition, pain, cancer related fatigue (CRF), body image, physical activity level, quality of life, and nutritional status in BCS undergoing hormone therapy. Methods and design: The HAPiMat Study is a randomized controlled clinical intervention trial comparing Mat Pilates with a control group. The primary outcomes are force production in different muscle groups, upper and lower limb flexibility, and gait and balance parameters. The secondary outcomes are quality of life, pain, cancer related fatigue, body image, sedentary behavior, functional capacity, physical activity level, nutritional intake, anthropometric measurements, and body composition. The safety of the Mat Pilates intervention and physical assessments are monitored throughout the intervention. Discussion: The strengths of this study are that the Pilates Method is mind-body training, which might ameliorate the side effects of breast cancer treatments, and that our intervention is systematized into sets, with the number of repetitions increased every eight weeks, enabling better results in the physical variables. Moreover, to date, no Pilates studies have focused on BCS undergoing hormone therapy only.