PURPOSE: We determined if a high-intensity aerobic exercise program would be safe, improve expected fitness and clinical outcomes, and alter exploratory phosphorous magnetic resonance spectroscopy (31 P MRS) outcomes in persons with multiple sclerosis (PwMS). METHODS: This open-label prospective pilot study compared 2 cohorts of ambulatory PwMS matched for age, sex and VO 2 max. Cohorts underwent 8-weeks of high-intensity aerobic exercise (MS-Ex, n=10) or guided stretching (MS-Ctr, n=7). Aerobic exercise consisted of four 30-minute sessions per week while maintaining ≥70% maximal heart rate. Changes in cardiorespiratory fitness, clinical outcomes, and 31 P MRS of tibialis anterior muscle (TA) and brain were compared. Cross-sectional 31 P MRS comparisons were made between all MS participants and a separate matched healthy control (HC) population. RESULTS: The MS-Ex cohort achieved target increases in VO 2 max (mean +12.7%, p=<0.001, between-group improvement p=0.03). One participant was withdrawn for exercise-induced syncope. The MS-Ex cohort had within-group improvements in fat mass (−5.8%, p=0.04), lean muscle mass (+2.6%, p=0.02), Symbol Digit Modalities Test (+15.1%, p=0.04), and cognitive subscore of the Modified Fatigue Impact Scale (MFIS: −26%, p=0.03) while only the physical subscore of the MFIS improved in MS-Ctr (−16.1%, p=0.007). 31 P MRS revealed significant within-group increases in MS-Ex participants in TA rate-constant of PCr recovery (k PCr ; +31.5%, p=0.03) and ATP/PCr (+3.2%, p=0.01), and near significant between-group increases in TA k PCr (p=0.05) but no significant changes in brain 31 P MRS following exercise. Cross-sectional differences existed between MS and HC brain PCr/Pi (4.61 ± 0.44, 3.93 ± 0.19 p=0.0019).