Background: Multiple sclerosis (MS) is a chronicinflammatory demyelinating disease of the central nervous system (CNS). Previous studies have shown that aerobic activity is inversely related to MS symptoms and may be restorative and possibly protective. Objectives: This study aimed to compare the effects of high-intensity functional training (HIFT) protocols and aerobic exercise on functional fitness as well as the cognitive aspect of female patients with multiple sclerosis. Methods: This quasi-experimentalandapplied clinical trial study consisted of all patients withMSregistered in anMSclinic. Among eligible individuals, 30 female RRMS patients were randomly and equally divided into three groups high-intensity functional training (n = 10); aerobic exercise (n = 10), and control group (n = 10). The forearm test, the 30-second standing test, and single leg stance test (SLST), The Timed Up and Go (TUG), expanded disability status scale (EDSS) were performed to assess physical factors as well as the 21-DAS questionnaire to assess cognitive aspects. Results: This study showed a meaningful difference between the intervention groups and the control group (P < 0.05), in the level of power in the upper body (P = 0.001), Lower torso strength (P = 0.001), Static balance (P = 0.001), Dynamic balance (P = 0.001). the psychological and behavioral components. Conclusions: Present study suggests that aerobic exercise and HIFT in women with MS can improve and further enhance physical function plus psychological and behavioral factors