This paper presents the evaluation of PID and fuzzy control logic for the lateral position control of a moving web in roll-to-roll (R2R) printed electronics. In addition, we report the implementation of computer simulation software that enables us to develop the control logic in a graphic user interface and to test the controller performance in 3D dynamic environment. A mathematical model of the web dynamics is described first to explain the lateral motion of a moving web. Based on the model, PID and fuzzy controllers are designed, and embedded in the simulation software. Under the simulation conditions for fabricating RFID antenna by R2R printing, the results indicate that the fuzzy controller shows a better performance and can be more suitable for R2R multi-layer printed electronics.