This paper proposes a new design exploration methodology, effectiveness-based design (EBD), to incorporate multidisciplinary analysis and design optimization, and uncertainty quantification earlier in the design process. The proposed EBD employs mission effectiveness objectives directly through physics-constrained operational analysis rather than relying on proxies such as aircraft weight, range, or fuel burn over a static mission or group of missions. Surrogate models are leveraged as part of EBD to achieve coupling between physics while being able to efficiently perform uncertainty quantification. To achieve EBD of an aircraft, a multiparameter performance code that accounts for variable engine features of a numerical and installed numerical propulsion system simulation coupled with a computational fluid dynamics analysis is executed in place of operational analysis. Various surrogate modeling methods are investigated for the approximated representation of the coupled physics, and it is found that the nondeterministic kriging is suitable to produce robust predictions requiring fewer off-design evaluations. To demonstrate the proposed framework, a generic fighter aircraft subject to uncertain flight and combat conditions is assessed through a combat mission.