Dynamic balance depends on the interaction between multiple brain networks and is impaired following Acquired Brain Injury (ABI). This study aims to characterize the brain functional and structural correlates of ABI-induced dynamic balance impairment and recovery at the chronic-phase following a rehabilitation treatment. 31 participants participated in a novel rehabilitation treatment composed of 22 sessions of perturbation training. Dynamic balance was assessed using the Community Balance and Mobility scale (CB&M) and the 10-Meter Walking Test (10MWT). Brain function was assessed based on resting-state fMRI scans which were analysed using independent component analysis (ICA), and regions of interest analyses. Brain volume was assessed using structural MRI and compared to age-matched and elderly participants. ICA revealed a reduction in component-related activation within the sensorimotor and cerebellar networks post-intervention (p < 0.035). Improvement in CB&M scale was associated with a reduction in FC within the cerebellar network (p = 0.023) and with baseline FC within the cerebellar-putamen (p = 0.002) and cerebellar-thalamic networks (p = 0.026). Improvement in 10MWT was associated with baseline FC within the cerebellar-putamen (p = 0.012) and cerebellar-cortical networks (p = 0.017, p = 0.004, p < 0.001and p = 0.005). A global brain volume reduction was found in the ABI-group when compared to the age-matched controls (p < 0.001), which was negatively associated with ABI chronicity, but not associated with CB&M scale. Our results show that dynamic balance recovery is associated with FC changes within and between the cerebellar and sensorimotor networks that are consistent with the contribution of modularity to balance control and recovery. The diffused atrophy post-ABI indicates that ABI led to a degenerative process.