Airworthiness certification is challenging for novel aircraft concepts. To avoid the significant cost associated with the redesign for certification compliance, incorporating certification requirements into early aircraft design is desired for unconventional aircraft. However, epistemic uncertainties arising from modeling assumptions, and aleatory uncertainties stemming from uncontrollable noise factors may have impacts on the certification analysis and certification-constrained design process. This paper presents an uncertainty quantification study based on a certification-constrained design and optimization study previously conducted for NASA’s Parallel Electric–Gas Architecture with Synergistic Utilization Scheme (PEGASUS) concept. The epistemic uncertainties are modeled through a set of multiplicative factors applied to intermediate disciplinary variables. The sensitivity analysis between design metrics and multiplicative factors reveals that uncertainties in stability and control derivatives can significantly affect certification constraint predictions, and uncertainties in drag approximations have considerable impacts on the vehicle sizing process. The aleatory uncertainties added to flight dynamics simulations include wind velocities and variations of weight and center of gravity. Four representative design candidates are evaluated for their robustness against aleatory uncertainties based on the Monte Carlo simulation performed on noise factors. The results show that aleatory uncertainties can affect the aircraft dynamic responses in flight test simulations, thus compromising certification compliance.