In this study we propose a non-invasive method to calculate blood flow by means of thermal infrared imaging and bio-heat transfer modeling. The method is able to provide high time-resolution series of cutaneous blood flow images with the same spatial resolution of the thermal images. The method was tested against a standard laser Doppler imaging system, which to date is considered the gold standard for non-invasive assessment of cutaneous blood flow, on both healthy subjects and patients suffering from systemic sclerosis (SSc; a pathological condition with microvessel endothelium injury). Twenty healthy subjects and twenty SSc patients simultaneously underwent laser Doppler and thermal imaging of the dorsum of the hand. A linear correlation between perfusion values obtained with the two methods was found for the healthy control group (R = 0.85, Pearson Product Moment Correlation). A significant correlation was not observed for the SSc patient group. The results of this study suggest that combined laser Doppler, thermal imaging and bio-heat transfer modeling could effectively discriminate between healthy vs. impaired conditions of the cutaneous tissue thermal properties and cutaneous vasculature. Such method, in addition to providing a potential effective imaging-based tool for a variety of biomedical and clinical applications ranging from diagnostics to treatment follow-up, may help the understanding of the morphological and functional impairment secondary to the disease. The thermal imaging-based method provided faster and better time-resolved imaging of cutaneous perfusion than standard laser Doppler techniques as the thermal cameras can provide up to 100 complete 524 x 524 pixel images per second, thus allowing real time monitoring of tissue perfusion rates.