The effect of natural convection on the uncertainty calculation of the MIKES dynamic gravimetric gas mass flow measurement system (DWS) is studied in this paper. The magnitude of the uncertainty component due to varying shear stress rate at the wall of the cylinder is studied theoretically at two different varying temperature models. Based on the obtained results, the contribution of the component may be significant, if the temperature difference between the wall of a gas cylinder and ambient air increases 1 K during one measurement cycle. Then the contribution of the shear stress can be above 92% of the combined standard uncertainty at the gas mass flow rate 0.1 mg s−1. Correspondingly, the contribution at the same temperature difference is below 1% at the mass flow rate 625 mg s−1. Applying the Monte Carlo uncertainty estimation method, the assumption of independent variables was shown to be reasonable.