One of the key challenges for adapting the roll-to-roll (R2R) process to flexible electronics production is to fulfill the tight registration requirements between layers. This study proposed a precise registration control for an R2R screen printing system based on a combination of registration error analysis, passive compensation, and active compensation. The registration error factors, such as film tension error, sintering error, reference alignment mark accuracy, screen printing error, and screen mask error, were evaluated. Meanwhile, with a refined correlation factor through the experiments, evaluation-based passive compensation was applied to the design layout for making a screen mask. Active compensation is based on combined control, which consists of the tension control and stage alignment control, reduces the registration error's varying term. As a result of passive and active compensation for polyethylene terephthalate film, achieving a machine direction registration error of 0 ± 9 µm (σ) and cross direction of 10 ± 4 µm (σ) was possible. The proposed R2R system with registration control was capable of accurate and precise registration over several hundred prints and was suitable for manufacturing flexible electronic devices.