The human brain has demonstrated the power to structurally change as a result of movement-based interventions. However, it is unclear whether these structural brain changes differ in autistic individuals compared to non-autistic individuals. The purpose of the present study was to pilot a randomized controlled trial to investigate brain, balance, autism symptom severity, and daily living skill changes that result from a biofeedback-based balance intervention in autistic adolescents (13–17 years old). Thirty-four autistic participants and 28 age-matched non-autistic participants underwent diagnostic testing and pre-training assessment (neuroimaging, cognitive, autism symptom severity, and motor assessments) and were then randomly assigned to six weeks of a balance-training intervention or a sedentary-control condition. After the six weeks, neuroimaging, symptom severity, and motor assessments were repeated. Results found that both the autistic and non-autistic participants demonstrated similar and significant increases in balance times with training. Further, individuals in the balance-training condition showed significantly greater improvements in postural sway and reductions in autism symptom severity compared to individuals in the control condition. Daily living scores did not change with training, nor did we observe hypothesized changes to the microstructural properties of the corticospinal tract. However, follow-up voxel-based analyses found a wide range of balance-related structures that showed changes across the brain. Many of these brain changes were specific to the autistic participants compared to the non-autistic participants, suggesting distinct structural neuroplasticity in response to balance training in autistic participants. All together, these findings suggest that biofeedback-based balance training may target postural stability challenges, reduce core autism symptoms, and influence neurobiological change. Future research is encouraged to examine the superior cerebellar peduncle in response to balance training and symptom severity changes in autistic individuals, as the current study produced overlapping findings in this brain region.