In this study, a multiple-input multiple-output feedforward controller for use with multiple-point fuel injection systems is applied to a diesel engine using an original control-oriented model. The target-tracking performance of this multiple-input multiple-output feedforward controller was then tested in terms of how well the controller adjusts the fuel delivery ratios to the pilot injection, pre-injection, main fuel injection, and the main fuel injection timing, and controls the in-cylinder peak pressure and its timing. Control experiments are conducted at different engine outputs and speeds while changing the targets of the in-cylinder peak pressure and its timing. The controller is able to track the varying targets within an acceptable error included in the original model. The calculation time, which is almost double that of a single-input single-output controller, is sufficiently fast to derive the applicable inputs.