The aim of this article is to present the theoretical and experimental work related to the vacuum system used for controlling the actuation of pneumatic valves in internal combustion engines in order to obtain a physical model of this system. In this context, these valves control the turbocharger operation in a two-stage sequential turbocharged diesel engine. With the purpose of providing the model with information, several characterization tests of the elements that integrate the vacuum system were performed. Related to the theoretical contents, two models of the vacuum system were developed and compared, either by using a 1D or a 0D approach. Within the experimental section the obtained instantaneous pressure in the actuator chamber of four air valves and two storage reservoirs of the circuit are measured and compared with the modeling results. Since the simulations show good agreement when comparing the instantaneous pressure evolutions and valve movement with the experimental data, the model can be used to predict the behavior of the vacuum system. Finally, the model is used to optimize the transient turbocharger sequential operation under real engine running conditions. The simulation results predict with accuracy the measurements acquired in an engine test bench. Therefore a consistent methodology has been established in order to reproduce the vacuum system behavior and can be used as a designing tool for complex applications devoted to engine controlling tasks.