In Japan, the Hypersonic Transport Propulsion System (HYPR) Project started in 1969 to develop technologies for the propulsion system of a Mach 5 Hypersonic Transport, sponsored by the Japanese Ministry of International Trade and Industry (MITI). The engine being studied is a combined-cycle engine composed of a turbo-jet engine for the lower speed range (Mach O-3) and a ram-jet engine for the higher speed range(Mach 2.55). In the HYPR project, CFD was found to be extremely helpful and important to understand the mechanisms of flow and heat transfer in the engine and to explain test data results. CFD has also contributed to some new technical innovations. This paper describes some examples of a CFD application in the HYPR engine development.