The paper reports a computer model for simulating dynamic responses in fuel rail of aircraft diesel engine. The fuel system is designed for use in a two-stroke compression-ignition engine with opposite pistons. The methodology of building a fuel system model in the AVL Hydsim program and the results of simulation studies are presented. Determination of dynamic phenomena in the fuel rail required the construction of a model of the entire supply system. It is a common rail system with a three-section positive displacement pump and electromagnetic fuel injectors. The system is also equipped with a PID regulator to maintain the present pressure in the fuel rail. For the purposes of the research, two structures of the fuel rail were developed. They differ in dimensions, spacing of the outlet ports and location of the high-pressure connection. The research allowed to determine the interactions between the geometry of the fuel rail and the supply method with the fuel pressure and injector mass flow rate. This will optimise the design of the fuel rail for the three-cylinder engine power supply system.