Improvement in technology is leading to complex systems in aerospace application. The data handling capabilities of the systems are increasing in the present technology. Current day interfaces demand large volume of data to be shared between the systems. It demands for high speed communication between the systems at affordable cost. Fiber channel based communication protocols on avionics systems has become the interconnection practices for new generation communication system. With its low latency, high reliability, distance transmission made it advantage to use for aerospace application. This paper describes the implementation of fiber channel based communication protocol on FPGA for avionics application.