Cortical volumetric analysis is widely used to study the anatomic basis of neurological deficits in patients with traumatic brain injury (TBI). However, patients with TBI-related lesions are often excluded from analysis, because cortical lesions may compromise the accuracy of reconstructed surfaces upon which volumetric measurements are based. Here, we propose a novel FreeSurfer-based lesion correction method and illustrate its impact on cortical volume measures in patients with chronic moderate-to-severe TBI. We performed MRI in 87 patients at mean+/−SD 10.9+/−9.1 years post-injury using a T1-weighted multi-echo MPRAGE sequence at 1 mm resolution. Following surface reconstruction, we parcellated the cerebral cortex into seven functional networks using FreeSurfer’s standard pipeline. Next, we manually labeled vertices on the cortical surface where lesions caused inaccuracies and removed them from network-based cortical volumetric measures. After performing this lesion correction procedure, we measured the surface area of lesion overlap with each network and the percent volume of each network affected by lesions. We identified 120 lesions that caused inaccuracies in the cortical surface in 46 patients. In these 46 patients, the most commonly lesioned networks were the limbic and default mode networks (95.7% each), followed by the executive control (78.3%), and salience (71.7%) networks. The limbic network had the largest average surface area of lesion overlap (4.4+/−3.7%) and the largest percent volume affected by lesions (12.7+/−9.7%). The lesion correction method has the potential to improve the accuracy of cortical volumetric measurements and permit inclusion of patients with lesioned brains in quantitative analyses, providing new opportunities to elucidate network-based mechanisms of neurological deficits in patients with TBI.