The effect of uncertainty in Reynolds-averaged Navier–Stokes (RANS) simulations is determined through the application of uncertainty quantification (UQ). In this study, the sensitivity of aerodynamic coefficients to uncertainty in the freestream turbulence intensity (FSTI) and surface roughness is computed for an airfoil (SC1095) and a rotorcraft fuselage model (Rotor-Body-Interaction-Mod7). A laminar–turbulent transition model has been extended to consider roughness-induced transition by incorporating an existing roughness-induced transition model. The current UQ analysis is based on the Monte Carlo method with the Gaussian distributions of uncertain input parameters. A surrogate model allows for incorporating the results of intensive RANS simulations into the Monte Carlo method. The surrogate model is generated using a cubic interpolation for a single-uncertain parameter or a radial basis function for multiple-uncertain parameters. The stochastic standard deviation is measured using combined FSTI and roughness uncertainties. The standard deviation of each aerodynamic coefficient depends on flow conditions (angle of attack, mean FSTI, and mean roughness) and the transition type (natural or separation-induced). The main source of output uncertainty is identified between the unknown FSTI and roughness under various flow conditions.