This paper presents a computer aided system, which can be used for simulation, design and operation of membrane-based gas separation processes. The computer aided system consists of a general model for the membrane-based gas separation process and a robust, reliable and flexible method of solution. The mathematical model consists of equations for the conservation of mass and momentum, which allows the consideration of effects such as pressure drops and various flow patterns within the permeator. The method of solution for the set of differential equations employs orthogonal collocation and decouples the set of equations by linearization in order to facilitate the calculation of sensitivities. In the current implementation, membrane modules with cocurrent or countercurrent flows and permeate pressure drops can be handled. Numerical results covering examples of simulation of gas separation units and effects of different variables on the design and operation of these processes are presented.