Computational fluid dynamics (CFD) is an essential tool with growing applications in many fields. In petrophysics, it is common to use computed tomography in those simulations, but in medicine, magnetic resonance imaging (MRI) is also being used as a basis for structural information. Wormholes are high-permeability structures created by the acidification of carbonate reservoirs and can impact reservoir production. CFD combined with MRI can benefit the study of wormholes in petrophysics, but combining both techniques is still a challenge. The objective of this study is to develop a pipeline for performing CFD in wormholes with MRI data. Using three samples of carbonate rocks acidified with 1.5% hydrochloric acid at 0.1, 1, and 10 ml/min, we acquired 300μm resolution T2-weighted images and experimental measurements of pressure data within flow rates of 5 to 50 ml/min. We applied cropping, bias field correction, non-local means denoising, and segmentation in the image processing step. For the 3D reconstruction, we used marching cubes to generate the surface mesh, the Taubin filter for surface smoothing, and boundary modeling with Blender. Finally, for the CFD, we generated volumetric meshes with cfMesh and used the OpenFOAM simpleFoam solver to simulate an incompressible, stationary, and laminar flow. We analyzed the effect of surface smoothing, estimating edge displacements, and measured the simulation pressure at the same flow rates as the experiments. Surface smoothing had a negligible impact on the overall edge position. For most flow rates, the simulation and experimental pressure measurements matched. A possible reason for the discrepancies is that we did not consider the surrounding porous media in the simulations. In summary, our work had satisfactory results, demonstrating CFD’s feasibility in studying wormholes using MRI.