Since the invention of functional magnetic resonance imaging (fMRI), thousands of studies in healthy and clinical samples have enlightened our understanding of the organization of cognition in the human brain and neuroplastic changes following brain disease and injury. Increasingly, studies involve analyses rooted in complex systems theory and analysis applied to clinical samples. Given the complexity in available approaches, concise descriptions of the theoretical motivation of network techniques and their relationship to traditional approaches and theory are necessary. To this end, this review concerns the use of fMRI to understand basic cognitive function and dysfunction in the human brain scaling from emphasis on basic units (or “nodes”) in the brain to interactions within and between brain networks. First, major themes and theoretical issues in the scientific study of the injured brain are introduced to contextualize these analyses, particularly concerning functional “brain reorganization.” Then, analytic approaches ranging from the voxel level to the systems level using graph theory and related approaches are reviewed as complementary approaches to examine neurocognitive processes following TBI. Next, some major findings relevant to functional reorganization hypotheses are discussed. Finally, major open issues in functional network analyses in neurotrauma are discussed in theoretical, analytic, and translational terms.