We present an innovative, inexpensive end-effector, the robot workcell, and the fuel cell components used to demonstrate the automated assembly process of a proton exchange membrane fuel cell stack. The end-effector is capable of handling a variety of fuel cell components including membrane electrode assemblies, bipolar plates and gaskets using vacuum cups mounted on level compensators and connected to a miniature vacuum pump. The end-effector and the fuel cell components are designed with features that allow an accurate component alignment during the assembly process within a tolerance of 0.02 in. and avoiding component overlapping which represents a major cause of overboard gas leaks during the fuel cell operation. The accurate component alignment in the stack is achieved with electrically nonconductive alignment pins permanently mounted on one fuel cell endplate and positioning holes machined on the fuel cell components and on the end-effector. The alignment pins feature a conical tip which eases the engagement between them and the positioning holes. A passive compliance system consisting of two perpendicularly mounted miniature linear blocks and rails allow compensating for the robot's limitations in accuracy and repeatability.