Estimation of permeability of porous media dates back to Henry Darcy (1856). The literature data on permeability are scattered, and this scatter not always can be attributed to the accuracy of experiment or simulation or to the sample variability. In this work, we prepare porous samples and determine their permeability experimentally. Hereafter, the samples are scanned in 3D using X-ray computed tomography, and the images are used for Stokes flow simulations using the lattice Boltzmann method with the simple bounce-back boundary condition. Careful execution of all steps in this combined experiment-simulation study resulted in an excellent agreement (<1%) between laboratory results and simulations. Here, experimental results are extensive and stable, while flow is simulated directly on three-dimensional images and without fitting parameters. Analyzing the conditions when experiments and simulations agree reveals a flaw affecting many experimental measurements with the out-of-sample placement of pressure ports, including industry standards. The flaw originates from (1) incorrect calculation of the applied pressure gradient, (2) omitting virtual part of the measured system, and (3) pressure loss at the sample–tube contact. Contrary to common wisdom, the relative magnitude of (3) is defined by the sample–tube diameter ratio and is independent of the size of sample pores. Removing or taking the flaw into account advances the understanding and control of flow-related processes in complex geometries.