We present an application of 3D X-ray computed microtomography for studying the influence of numerical cementation on flow in a cement-lined rough-walled fracture. The imaged fracture geometry serves as input for flow modeling using a combination of the level set and the lattice Boltzmann methods to characterize the capillary-dominated fluid displacement properties and the relative permeability of the naturally cemented fracture. We further numerically add cement to the naturally cement-lined fracture to quantify the effect of increasing cement thickness and diminishing aperture on flow properties. Pore space geometric tortuosity and capillary pressure as a function of water saturation both increase with the numerically increased fracture cement thickness. The creation of unevenly distributed apertures and cement contact points during numerical cement growth causes the wetting and non-wetting fluids to impede each other, with no consistent trends in relative permeability with increasing saturation. Tortuosity of wetting and non-wetting fluid phases exhibits none to poor correlation with relative permeability and thus cannot be used to predict it, contrary to previous findings in smoother fractures.