COVID-19 may increase the risk of acute ischemic stroke that can cause a loss of upper limb function, even in patients with low risk factors. However, only individual cases have been reported assessing different degrees of hospitalization outcomes. Therefore, outpatient recovery profiles during rehabilitation interventions are needed to better understand neuroplasticity mechanisms required for upper limb motor recovery. Here, we report the progression of physiological and clinical outcomes during upper limb rehabilitation of a 41-year-old patient, without any stroke risk factors, which presented a stroke on the same day as being diagnosed with COVID-19. The patient, who presented hemiparesis with incomplete motor recovery after conventional treatment, participated in a clinical trial consisting of an experimental brain-computer interface (BCI) therapy focused on upper limb rehabilitation during the chronic stage of stroke. Clinical and physiological features were measured throughout the intervention, including the Fugl-Meyer Assessment for the Upper Extremity (FMA-UE), Action Research Arm Test (ARAT), the Modified Ashworth Scale (MAS), corticospinal excitability using transcranial magnetic stimulation, cortical activity with electroencephalography, and upper limb strength. After the intervention, the patient gained 8 points and 24 points of FMA-UE and ARAT, respectively, along with a reduction of one point of MAS. In addition, grip and pinch strength doubled. Corticospinal excitability of the affected hemisphere increased while it decreased in the unaffected hemisphere. Moreover, cortical activity became more pronounced in the affected hemisphere during movement intention of the paralyzed hand. Recovery was higher compared to that reported in other BCI interventions in stroke and was due to a reengagement of the primary motor cortex of the affected hemisphere during hand motor control. This suggests that patients with stroke related to COVID-19 may benefit from a BCI intervention and highlights the possibility of a significant recovery in these patients, even in the chronic stage of stroke.