Neuroimaging studies show reorganization of neural resources in older adults may compensate for cognitive decline. To effectively evaluate neural compensation, we proposed a data-driven independent component analysis method, and tested the measure through a longitudinal study. Twenty-six healthy older adults participated in a 6-week physical exercise program. Gait speed, cognitive function, and fMRI during a challenging memory task were measured before and after the program. Results showed a positive correlation between the compensatory ability measure and gait speed at baseline. Physical exercise improved gait speed, cognition, and compensatory ability through increased involvement of motor-related networks in conducting the cognitive task.