A successful store separation analysis tool, MSAP(Multi-body Separation Analysis Program) has been applied to F/A-18C/JDAM CFD Challenge Ⅱ. The challenge was devised to challenge CFD community to use CFD methodologies to predict and match the trajectory of a JDAM MK-84 separating from F/A-l8C. Trajectory simulations for two flight conditions were performed. Comparison between computed and measured flight trajectories for both conditions shows a good agreement.