This dissertation addresses model form uncertainty quantification, non-deterministic simulations, and sensitivity analysis of the results of these simulations, with a focus on application to analysis of unmanned aircraft systems. The model form uncertainty quantification utilizes equation error to estimate the error between an identified model and flight test results. The errors are then related to aircraft states, and prediction intervals are calculated. This method for model form uncertainty quantification results in uncertainty bounds that vary with the aircraft state, narrower where consistent information has been collected and wider where data are not available. Non-deterministic simulations can then be performed to provide uncertainty quantified estimates of the system performance. The model form uncertainties could be time varying, so multiple sampling methods were considered. The two methods utilized were a fixed uncertainty level and a rate bounded variation in the uncertainty level. For analysis using fixed uncertainty level, the corner points of the model form uncertainty were sampled, providing reduced computational time. The second model better represents the uncertainty but requires significantly more simulations to sample the uncertainty. The uncertainty quantified performance estimates are compared to estimates based on flight tests to check the accuracy of the results. Sensitivity analysis is performed on the uncertainty quantified performance estimates to provide information on which of the model form uncertainties contribute most to the uncertainty in the performance estimates. The proposed method uses the results from the fixed uncertainty level analysis that utilizes the corner points of the model form uncertainties. The sensitivity of each parameter is estimated based on corner values of all the other uncertain parameters. This results in a range of possible sensitivities for each parameter dependent on the true value of the other parameters. / Ph. D.