Among the alternatives to the use of fossil diesel fuel, dual fuel combustion, leveraging hydrogen as the low-reactivity fuel, represents a promising approach for both reducing pollutant emissions and improving brake thermal efficiency. In addition, this innovative combustion mode requires minimal modifications to the existing Diesel engines architecture. This study was conducted on a Diesel engine (naturally aspirated, 3-cylinder, 1 L, direct injection), properly modified by the authors to operate in dual fuel mode with port fuel injection of hydrogen. A set of experimental data was used to calibrate the 1D and the 3D-CFD models for both Diesel and diesel-hydrogen dual fuel configurations. The AVL FIRE M 3D-CFD software was employed to model diesel injection and combustion, while the gas exchange process was analyzed by GT-Power. The validated 3D-CFD model was then leveraged to optimize the baseline diesel injection strategy in dual fuel mode, minimizing diesel consumption while maintaining stable combustion and comparable performance with respect to the baseline Diesel engine. Notably, the analysis highlights that, at low loads, where hydrogen energy fraction is limited, a diesel injection strategy consisting of two fuel pulses is required to ensure stable ignition. However, as the hydrogen contribution increases, the main injection can be reduced or eliminated, with the pilot injection alone being sufficient to ignite the premixed charge, without compromising engine efficiency. This optimized strategy enabled a simultaneous reduction in diesel usage, up to −62.6%, and a marked decrease in emissions, with the best reductions reaching −62.5% for CO₂, −81.1% for CO, and −31.6% for NOₓ.