Stroke is the second leading cause of death worldwide and the third leading cause of death in the USA. A clinically useful biomarker for the diagnosis of stroke does not currently exist. Biomarkers could improve stroke care by allowing early diagnosis by non-expert clinical providers, serial monitoring of patients, and rapid assessment of severity of brain injury. With the introduction of highly advanced multidimensional separation techniques coupled with high throughput genomics/proteomics platforms, several components of the pathophysiological and biochemical pathways have been elucidated in the areas of brain trauma. A major outcome of these approaches is the discovery of biomarkers that would have important applications in diagnosis, prognosis, and even development of experimental neuroprotective drugs that have been used in different paradigms of brain injury. In this paper, we reviewed the recent advances of current and novel brain injury protein biomarkers and their utilities in different models of brain injury with an emphasis on stroke, an area that has been understudied. This will include the utility of neuroproteomics/neurosystems biology analysis as a novel discipline leading to the identification of novel biomarkers that can reach the pipeline of bench side. Additionally, an outline of biomarker-based management of traumatic brain injury and stroke patient assessments of therapeutic interventions has been included. Finally, comparison of current biomarker occurrence between preclinical models and biomarker data from human clinical studies for stroke has been summarized.