Purpose: This study was conducted aiming to investigate the effect of selected TRX and Pilates training on balance parameters, fatigue index, and quality of life in female patients of multiple sclerosis. Method: In this study, 30 female patients with MS in Isfahan city with an average age of 37.41 ± 7.57 years and a history of MS of 11.31 ± 3.77 years and an Expanded Disability Status Scale of 0.84 ± 1.81 were placed in three groups including control, TRX and Pilates groups. The training program consisted of eight weeks including 3 sessions of 60 minutes of exercise per week. In order to investigate balance, fatigue, and quality of life, the Berg test, Fatigue Severity Scale, and Multiple Sclerosis Quality of Life were used respectively. SPSS version 25 software was used for statistical analysis. Results: The results of this study have shown that both exercise programs have led to a significant improvement in the mean parameters of balance (P < 0.005), fatigue (P < 0.005), and quality of life (P < 0.001). Conclusions: Considering the noticeable impact of these training protocols on the quality of life, balance and fatigue, these interventions can be considered as an efficient and cost-effective methods to improve health condition in MS patients.