Advancing therapeutics for traumatic brain injury (TBI) remains a challenge, necessitating testable targets with interventions appropriately timed to intercede on evolving secondary insults. Neuroproteomics provides a global molecular approach to deduce the complex post-translational processes that underlie secondary events after TBI. Yet method advancement has outpaced approaches to interrogate neuroproteomic complexity, in particular when addressing the well-recognized temporal evolution of TBI pathobiology. Presented is a detailed account of the temporal neuroproteomic response to mild-moderate rat controlled cortical impact within perilesioned somatosensory neocortex across the first two weeks after injury. Further, this investigation assessed use of artificial neural network and functional enrichment analyses to discretize the temporal response across some 2047 significantly impacted proteins. Results were efficiently narrowed onto ion transporters with phenotypic relevance to abnormal GABAergic transmission and a delayed decline amenable to intervention under managed care conditions. The prototypical target potassium/chloride co-transporter 2 (KCC2 or SLC12A5) was investigated further with the KCC2-selective modulator CLP290. Guided by post-translational processing revealed one-day after insult to precede KCC2 protein loss a day after, CLP290 was highly effective at restoring up to 70% of lost KCC2 localization, which was significantly correlated with recovery of sham-level function in assessed somatosensory behavioral tasks. The timing of administration was important, with no significant improvement observed if given earlier, one-hour after insult, or later when KCC2 protein decline begins. Results portend importance for a detailed post-translational characterization when devising TBI treatments, and support the therapeutic promise of KCC2-targeted CLP290 intervention for positive functional recovery after brain injury.