This paper presents the development of an integrated approach which targets the aerodynamic design of separate-jet exhaust systems for future gas-turbine aero-engines. The proposed framework comprises a series of fundamental modeling theories which are applicable to engine performance simulation, parametric geometry definition, viscous/compressible flow solution, and design space exploration (DSE). A mathematical method has been developed based on class-shape transformation (CST) functions for the geometric design of axisymmetric engines with separate-jet exhausts. Design is carried out based on a set of standard nozzle design parameters along with the flow capacities established from zero-dimensional (0D) cycle analysis. The developed approach has been coupled with an automatic mesh generation and a Reynolds averaged Navier–Stokes (RANS) flow-field solution method, thus forming a complete aerodynamic design tool for separate-jet exhaust systems. The employed aerodynamic method has initially been validated against experimental measurements conducted on a small-scale turbine powered simulator (TPS) nacelle. The developed tool has been subsequently coupled with a comprehensive DSE method based on Latin-hypercube sampling. The overall framework has been deployed to investigate the design space of two civil aero-engines with separate-jet exhausts, representative of current and future architectures, respectively. The inter-relationship between the exhaust systems' thrust and discharge coefficients has been thoroughly quantified. The dominant design variables that affect the aerodynamic performance of both investigated exhaust systems have been determined. A comparative evaluation has been carried out between the optimum exhaust design subdomains established for each engine. The proposed method enables the aerodynamic design of separate-jet exhaust systems for a designated engine cycle, using only a limited set of intuitive design variables. Furthermore, it enables the quantification and correlation of the aerodynamic behavior of separate-jet exhaust systems for designated civil aero-engine architectures. Therefore, it constitutes an enabling technology toward the identification of the fundamental aerodynamic mechanisms that govern the exhaust system performance for a user-specified engine cycle.