Breast cancer treatment causes upper extremity (UE) impairments. This study aims to assess the efficacy of Pilates-based exercises (PE) in comparison with combined exercise (CE) and home exercise (HE) groups, in the rehabilitation of UE disorders related with breast cancer treatment. Fifty-five patients were randomly allocated to PE, CE (consisting of strengthening, stretching and range of motion [ROM] exercises) and HE groups (consisting of CE group exercises). Pain (using visual analogue scale), ROM (using digital goniometer), muscle strength (using dynamometer and pinch gauge), functional status (using Constant-Murley scale and Disabilities of the Arm, Shoulder and Hand scale) were evaluated before and after intervention. For data analyses (using spss 21 version), one-way ANOVA, paired samples t-test and Kruskal-Wallis test were performed (p ≤ .05 was considered statistically significant). The data obtained in this study revealed significant improvements in almost all the parameters measured in the PE and CE groups, and some improvements were superior to HE group. PE seemed to have resulted similar improvements in pain, muscle strength and functional status when compared to CE group. Therefore, PE seems to be an effective method of rehabilitation of patients with UE disorders related with breast cancer treatment, and might be considered for use as an alternative to CE in this population.