The objective of this work was to develop an analysis methodology for engine intake manifolds in Formula SAE prototypes, addressing the three-dimensional (3D) airflow characteristics within these complex geometries. Air flow modelling via one-dimensional (1D) computational fluid dynamics (CFD) software does not capture properly the manifold airflow characteristics and may lead to unrealistic engine performance prediction. On the other hand, the use of purely 3D-CFD simulations of intake manifold isolated from engine, without adequate boundary conditions, also does not conduct to realistic behavior. To address these issues, a 1D-CFD transient analysis model was created using GT-Suite software from Gamma Technologies, which provided boundary conditions for the engine’s airflow demand to Ansys Fluent, the 3D-CFD simulation software. Ansys Fluent, in turn, returned the actual conditions imposed by the manifold geometry to the 1D model, enabling a bidirectional simulation that enhances the evaluation of the engine’s functional parameters and internal components. This methodology relies on the characterization of dimensional engine parameters, calibration of valve flow coefficients for intake and exhaust valve flow through CFD analysis, mesh convergence studies, and appropriate selection of solvers and turbulence models based on expected velocity and mesh size. It aims to improve the team’s understanding of potential optimizations in both engine and intake manifold design, encouraging exploration of enhancements throughout the prototype’s lifecycle. Additionally, it establishes a robust CFD methodology that supports precise design decisions while allowing for future refinements to the approach. The application of this methodology resulted in a more realistic numerical representation of the engine’s operational behavior, facilitating the visualization of various fluid dynamics phenomena, such as velocity and pressure contours, streamlines, and air distribution within the intake manifold under defined operating conditions of engine speed and load. Consequently, it reduced discrepancies in volumetric efficiency and torque calculations compared to standalone 1D simulations.