The present study adopted a randomized controlled trial design and examined the effect of a physical activity behavioral intervention on cognitive and walking performance among persons with MS who have mild or moderate disability status. A total of 82 MS patients were randomly allocated into intervention or wait-list control conditions. The intervention condition received a theory-based program for increasing physical activity behavior that was delivered via the Internet, and one-on-one video chat sessions with a behavior-change coach. Participants completed self-report measures of physical activity and disability status, and underwent the oral Symbol Digit Modalities Test (SDMT) and 6-minute walk (6MW) test before and after the 6-month period. Analysis using mixed-model ANOVA indicated a significant time × condition × disability group interaction on SDMT scores (p = 0.02, partial-η (2) = 0.08), such that persons with mild disability in the intervention condition demonstrated a clinically meaningful improvement in SDMT scores (~6 point change). There was a further significant time × condition interaction on 6MW distance (p = 0.02, partial-η (2) = 0.07), such that those in the intervention condition demonstrated an increase in 6MW distance relative to those in the control group. The current study supports physical activity as a promising tool for managing cognitive impairment and impaired walking performance in persons with MS, and suggests that physical activity might have specific effects on cognition and non-specific effects on walking performance in this population.