Hardware-In-Loop simulation (HILS) is the only platform used to validate the on-board software for aerospace applications along with the other flight subsystems. HILS system should be capable of high speed data acquisition, integration with traditional interface protocols to latest technology based interfaces. PCI/ISA based computer system is only able to integrate with limited I/O resources and limited speed. Compact Peripheral Interface (cPCI) protocol is superset of PCI architecture which follows state-of-the art technology that significantly eases the system design task, shortening the design cycle, time-to-market and robust mechanical form factor than desktop computer. This paper provides technical overview of the cPCI system for HILS and real time modeling and simulation software development. Total integration cycle of the system under HILS environment and testing with each HILS configuration is also explained.