We develop a semi-analytical model of transient fluid flow in a 2D layered permeable medium with cross-flow between adjacent layers. It is shown that the pressure satisfies a diffusion equation to leading order, even when the non-linear term and gravity are included in the mathematical model. The solution is based on an analytical expression in the transform domain for the fluid pressure in terms of interfacial flux functions; the algorithm to compute the flux functions accepts an arbitrary number of formation layers. We show some benchmark tests that validate the general model; the model is then applied to an example derived from experiments. Numerical experiments confirm the significance of the cross-flow in a particular scaling of the ratio of permeabilities and quantify the influence of the various physical parameters.