A method for computing or estimating relative permeability for fractional multi-phase, multi-component fluid flow through a porous medium, which employs a 3D digital representation of a porous medium and a computational fluid dynamics method to calculate flow rates, pressures, saturations, velocities and other flow parameters, is described. The method employs a unique method which integrates a precursor simulation used to generate a set of variables like pressure, saturation and velocity distribution associated with a selected storage plane in the 3D digital representation of a porous medium, which variables are used as inlet condition in the workflow of a second simulation that can generate values of fractional flow rates, pressures, saturations, velocities, or other parameters of wetting and non-wetting phases, which can be used to compute or estimate relative permeability values or other fluid transport properties of the porous medium. Computerized systems and programs for performing the method are also provided.