In internal combustion engines, cycle-to-cycle and cylinder-to-cylinder variations of the combustion process have been shown to negatively impact the fuel efficiency of the engine and lead to higher exhaust emissions. The combustion variations are generally tied to differences in the composition and condition of the trapped mass throughout each cycle and across individual cylinders. Thus, advanced engines featuring exhaust gas recirculation, flexible valve actuation systems, advanced fueling strategies, and turbocharging systems are prone to exhibit higher variations in the combustion process. In this study, the cylinder-to-cylinder variations of the combustion process in a dual-fuel internal combustion engine leveraging late intake valve closing are investigated and a model to predict and address one of the root causes for these variations across cylinders is developed. The study is conducted on an inline six-cylinder heavy-duty dual-fuel engine equipped with exhaust gas recirculation, a variable geometry turbocharger, and a fully flexible variable intake valve actuation system. The engine is operated with late intake valve closure timings in a dual-fuel combustion mode in which a high reactivity fuel is directly injected into the cylinders and a low reactivity fuel is port injected into the cylinders. The cylinder-to-cylinder variations observed in the study have been associated with the maldistribution of the port-injected fuel, which is exacerbated at late intake valve timings. The resulting difference in indicated mean effective pressure between the cylinders ranges from 9% at an intake valve closing of 570° after top dead center to 38% at an intake valve closing of 620° after top dead center and indicates an increasingly uneven fuel distribution. The study leverages both experimental and simulation studies to investigate the distribution of the port-injected fuel and its impact on cylinder-to-cylinder variation. The effects of intake valve closing as well as the impact of intake runner length on fuel distribution were quantitatively analyzed, and a model was developed that can be used to accurately predict the fuel distribution of the port-injected fuel at different operating conditions with an average estimation error of 1.5% in cylinder-specific fuel flow. A model-based control strategy is implemented to adjust the fueling at each port and shown to significantly reduce the cylinder-to-cylinder variations in fuel distribution.