Background Rehabilitative treatments that promote neuroplasticity are believed to improve recovery after stroke. Animal studies have shown that cardiovascular exercise (CE) promotes neuroplasticity but the effects of this intervention on the human brain and its implications for the functional recovery of patients remain unclear. The use of biomarkers has enabled the assessment of cellular and molecular events that occur in the central nervous system after brain injury. Some of these biomarkers have proven to be particularly valuable for the diagnosis of severity, prognosis of recovery, as well as for measuring the neuroplastic response to different treatments after stroke. Objectives To provide a critical analysis on the current evidence supporting the use of neurophysiological, neuroimaging, and blood biomarkers to assess the neuroplastic response to CE in individuals poststroke. Results Most biomarkers used are responsive to the effects of acute and chronic CE interventions, but the response appears to be variable and is not consistently associated with functional improvements. Small sample sizes, methodological variability, incomplete information regarding patient’s characteristics, inadequate standardization of training parameters, and lack of reporting of associations with functional outcomes preclude the quantification of the neuroplastic effects of CE poststroke using biomarkers. Conclusion Consensus on the optimal biomarkers to monitor the neuroplastic response to CE is currently lacking. By addressing critical methodological issues, future studies could advance our understanding of the use of biomarkers to measure the impact of CE on neuroplasticity and functional recovery in patients with stroke.