Wave phenomena that occur inside the intake manifold can either increase or decrease the volumetric efficiency of internal combustion engines. In this paper, numerical and experimental studies were performed to investigate the influence of intake manifold system components such as a Helmholtz resonator, plenum, and primary and secondary pipes on the air mass flow rate through the intake manifold. In order to calculate the natural frequency of the components, the transfer matrix method (TMM) and the lumped parameter model (LPM) were used. The numerical solutions were calculated using a one-dimensional computational code based on the characteristic method. Experimental tests were conducted using a flow test bench with a four-cylinder engine in non-stationary conditions with two operating intake valves. The flow test bench reproduces the pulsating phenomena in the intake system, which was composed of an engine cylinder head — driven by an electric motor connected to the camshaft through a timing belt — mounted in an equalization tank. Numerical and experimental results were compared, and good agreement was found, thus confirming the numerical code’s capacity to reproduce this type of phenomenon. Both LPM and TMM analytical methods were able to calculate the system’s frequency with relative accuracy. The insertion of resonators increased the air mass flow rate by up to 80.05%. The resonator responses were not limited only to the point of natural frequency but to a wide frequency range. The design of the compact Helmholtz resonator proved to be very efficient since it made it possible to increase the mass flow rate by up to 79.23% and considering that its design takes up relatively little space for its installation.