In the present study, a rigorous dynamic and controloriented model is developed towards accurately describing the autonomous operation of a methanol reformingfuel cell power system (up to 5 kW(el)). The system consists of an autothermal steam reformer that provides hydrogen to a polymer electrolyte membrane (PEM) fuel cell. A purification stage (preferential oxidation reactor) intercedes between the steam reformer and the fuel cell and maintains CO levels below 10-50 ppm, while a heatexchanging network (comprising of two coolers and a burner) is employed towards managing a well-balanced autothermal operation. The proposed dynamic model is developed on the basis of describing accurately the evolving chemical and electrochemical interactions between the subsystems and utilizes a group of partial/ordinary differential equation (reactors and heat exchangers) along with a set of non-linear equations (reaction kinetics and currentvoltage dependence). Based on the system main operating features, a control structure through the implementation of PI controllers is proposed for the control of (a) the reformer feed and exit temperature through methanol burning and steam reformer feed flowrate manipulation respectively, (b) CO concentration through O-2/CO feed ratio manipulation, (c) power production (specified by the fuel cell operation current) through methanol reformer feed and (d) subsystem exit temperatures through coolant flowrate manipulation. An overall simulation case study reveals the proper selection of system manipulated and controlled variables towards achieving the applied operating setpoints, where it is shown that the system sustains a flexible operation, along with fast start-up and dynamic transients.