Advances in neuroimaging technology, like functional near-infrared spectroscopy (fNIRS), support the evaluation of task-dependent brain activity during functional tasks, like balance, in healthy and clinical populations. To date, there have been no studies examining how interventions, like yoga, impact task-dependent brain activity in adults with chronic acquired brain injury (ABI). This pilot study compared eight weeks of group yoga (active) to group exercise (control) on balance and task-dependent neural activity outcomes. Twenty-three participants were randomized to yoga (n = 13) or exercise groups (n = 10). Neuroimaging and balance performance data were collected simultaneously using a force plate and mobile fNIRS device before and after interventions. Linear mixed-effects models were used to evaluate the effect of time, time x group interactions, and simple (i.e., within-group) effects. Regardless of group, all participants had significant balance improvements after the interventions. Additionally, regardless of group, there were significant changes in task-dependent neural activity, as well as distinct changes in neural activity within each group. In summary, using advances in sensor technology, we were able to demonstrate preliminary evidence of intervention-induced changes in balance and neural activity in adults with ABI. These preliminary results may provide an important foundation for future neurorehabilitation studies that leverage neuroimaging methods, like fNIRS.