Objective: Traumatic brain injury (TBI) is associated with impairments in processing speed as well as higher-level cognitive functions that depend on distributed neural networks, such as regulating and sustaining attention. Although exogenous alerting cues have been shown to support patients in sustaining attentive, goal-directed behavior, the neural correlates of this rehabilitative effect are unclear. The purpose of this study was to explore the effects of moderate to severe TBI on activity and functional connectivity in the well-documented right-lateralized frontal-subcortical-parietal sustained attention network, and to assess the effects of alerting cues. Method: Using multivariate analysis of fMRI data, TBI patients and matched neurologically healthy (NH) comparison participants were scanned as they performed the Sustained Attention to Response Task (SART) in 60-s blocks, with or without exogenous cueing through brief auditory alerting tones. Results: Results documented inefficient voluntary control of attention in the TBI patients, with reduced functional connectivity in the sustained attention network relative to NH participants. When alerting cues were present during the SART, however, functional connectivity increased and became comparable to activity patterns seen in the NH group. Conclusions: These findings provide novel evidence of a neural mechanism for the facilitatory effects of alerting cues on goal-directed behavior in patients with damaged attentional brain systems, and support their use in cognitive rehabilitation.