Multi-layer boundary value problems have received a great deal of attention in the past few years. This is due to the fact that they model many engineering applications. Examples of applications include fluid flow though multi-layers porous media such as ground water and oil reservoirs. In this work, we present a new method for solving multilayer boundary value problems. The method is based on an efficient adaption of the classical shooting method, where boundary value problems are solved for by means of solving a sequence of initial value problems. Illustration of the method is presented on application to fluid flow through multi-layer porous media. The examples presented suggested that the method is reliable and accurate.