Store separation analyses are carried out in order to estimate the safe separation envelope for external stores carried on military aircrafts by varying the flight/ejection conditions. Typical separation analysis considers either only the store motion beyond the end-of-stroke (EoS), or solves the EoS conditions with predefined ejection forcing that are assumed to be unaltered with respect to flight/ejection conditions. There exists a gap in the literature in modeling the EoS conditions and precise ejection loads. Data from ground and flight tests show that, dynamic responses of a store differ beyond acceptable limits where aerodynamics and aircraft elasticity are the two main sources of this miscorrelation. In order to have a reliable mathematical model that modifies the ground test data to have a reasonable correlation with the real ejection case, not only ejector and store dynamics but also store aerodynamics, aircraft aerodynamics, aircraft rigid body dynamics, aircraft elasticity should be considered. To show the effects of aircraft deformation on the EoS store conditions, first of all, a methodology that can be used to estimate the ejection loads and EoS conditions of the store more precisely is presented. For the purpose of visualizing the aeroelastic effects on store ejection dynamics, various virtual test cases are handled by changing wing torsional stiffness values and store mounting station positions along aircraft longitudinal axis. The acceleration responses of the store, obtained with and without the inclusion of aeroelastic effects, are used to emphasize the effects of aeroelasticity on ejection.