The relationship between abdominal subcutaneous adipose tissue thickness (aSAT), body fat percentage (BFP), waist-to-hip ratio (WHR) and body mass index (BMI) and outcome measures of neurological deficit and functional recovery was evaluated in obese subacute stroke patients before and after neurorehabilitation. Decreased National Institutes of Health Stroke Scale (p = 0.0001) and modified Rankin Scale (mRS) (p= 0.002) scores, as well as increased Barthel Index (p= 0.0001) scores were detected after neurorehabilitation. Decreased BMI, aSAT, BFP and WHR observed after neurorehabilitation did not penalize the overall functional recovery as shown by correlations between the clinical measure scores and fat mass indices. The correlation observed after neurorehabilitation between BMI and mRS (rho = 0.4526, p < 0.05) suggests that a high BMI may compromise functional recovery. Monitoring of body fat mass indices may provide information aimed at improving the disability of obese stroke patients.