This paper presents the application of rapid prototyping electronic control unit (ECU) to fuel injection and ignition control of electronic fuel injection motorcycle engine by using Model-Based environment. As a scene on state of the art, it is famous accepted that the MATLAB Model-Based environment is an efficient development platform for engine management systems (EMS). These come from several benefits: (1) System level design environment, (2) Real-time simulation, and (3) Model to chip technology during rapid prototyping ECU development process. Therefore, this research uses these advantages to study the rapid prototyping controller (RPC) of a SI engine for decreasing time and cost requirements of development process. The target vehicle is a scooter with a four-stroke 125 cc. single cylinder engine. A systematic architecture of EFI (Electronic Fuel Injection) by using Motorola MC68376 micro-controller is utilized as a master controller and MATLAB/Simulink/Stateflow as software kernel to design the control strategy of ignition timing and fuel injection. The engine test results show that this RPC is an efficient tool and easy to obtain better engine performance.