Background: Image-based computational hemodynamic modeling and simulations are important for personalized diagnosis and treatment of cardiovascular diseases. However, the required patient-specific boundary conditions are often not available and need to be estimated.Methods: We propose a pipeline for estimating the parameters of the popular three-element Windkessel (WK3) models (a proximal resistor in series with a parallel combination of a distal resistor and a capacitor) of the aortic arch arteries in patients receiving thoracic endovascular aortic repair of aneurysms. Pre-operative and post-operative 1-week duplex ultrasound scans were performed to obtain blood flow rates, and intra-operative pressure measurements were also performed invasively using a pressure transducer pre- and post-stent graft deployment in arch arteries. The patient-specific WK3 model parameters were derived from the flow rate and pressure waveforms using an optimization algorithm reducing the error between simulated and measured pressure data. The resistors were normalized by total resistance, and the capacitor was normalized by total resistance and heart rate. The normalized WK3 parameters can be combined with readily available vessel diameter, brachial blood pressure, and heart rate data to estimate WK3 parameters of other patients non-invasively.Results: Ten patients were studied. The medians (interquartile range) of the normalized proximal resistor, distal resistor, and capacitor parameters are 0.10 (0.07–0.15), 0.90 (0.84–0.93), and 0.46 (0.33–0.58), respectively, for common carotid artery; 0.03 (0.02–0.04), 0.97 (0.96–0.98), and 1.91 (1.63–2.26) for subclavian artery; 0.18 (0.08–0.41), 0.82 (0.59–0.92), and 0.47 (0.32–0.85) for vertebral artery. The estimated pressure showed fairly high tolerance to patient-specific inlet flow rate waveforms using the WK3 parameters estimated from the medians of the normalized parameters.Conclusion: When patient-specific outflow boundary conditions are not available, our proposed pipeline can be used to estimate the WK3 parameters of arch arteries.