Over the last years, automotive industries drove a great amount of research in the field of advanced combustion techniques minimizing carbon dioxide emissions. The so-called Low-Temperature Combustions (LTC), characterized by the self-ignition of highly premixed air-fuel mixtures, represent a promising solution to achieving high efficiency and ultralow emissions of nitrogen oxides (NOx) and particulate matter. Among these, gasoline Partially Premixed Combustion (PPC), obtained through the high-pressure direct injections of gasoline, showed a good potential for the simultaneous reduction of pollutants and emissions in compression ignited engines. However, when multiple injections per cycle are performed (with hydraulic-assisted needle opening), combustion stability might be compromised by the wave effects in the hydraulic system, which produce incoherence between the requested and injected fuel. This work presents a model-based pressure waves reconstruction strategy, based on a control-oriented model of the high-pressure common rail injection system fueled with gasoline. To determine the hydraulic system’s behavior during the injection process, a specifically designed flushing bench with a high-frequency acquisition system has been developed. Experimental activities have been carried out to highlight fuel pressure fluctuations with single and double injection patterns. Through the analysis of the acquired data, the key parameters (characteristic of the system) have been identified and the accuracy of pressure waves reconstruction has been evaluated, always returning errors lower than 2% between measured and estimated instantaneous pressures. Different fuel types, injectors, and rail positions have been tested to highlight the robustness of the approach. Based on the instantaneous pressure trace estimated with the control-oriented model, a fuel quantity Fluctuation Correction Strategy (FQC), implementable on a standard engine Electronic Control Unit (ECU), has been developed. The obtained results confirm the potential to reduce fuel quantity oscillations in multiple-injections systems.