Internal resistance is a critical parameter of the thermal behavior of Li-ion battery cells. This paper proposes an innovative way to deal with the uncertainties related to this physical parameter using experimental data and numerical simulation. First, a CFD model is validated against an experimental configuration representing the behavior of heated Li-ion battery cells under constant discharging current conditions. Secondly, an Uncertainty Quantification based methodology is proposed to represent the internal resistance and its inherent uncertainties. Thanks to an accurate and fast to compute surrogate model, the impact of those uncertainties on the temperature evolution of Li-ion cells is quantified. Finally, a Bayesian inference of the internal resistance model parameters using experimental measurements is performed, permitting to reduce the prediction uncertainty by almost 95% for some temperatures of interest.