One of the most important requirements when using roll-to-roll printing equipment for multilayer printing is register control. Because multilayer printing requires a printing accuracy of several microns to several tens of microns, depending on the devices and their sizes, precise register control is required. In general, the register errors vary with time, even for one revolution of the plate cylinder. Therefore, more information about the register errors in one revolution of the plate cylinder is required for more precise register control, which is achieved by using multiple register marks in a single revolution of the plate cylinder. By using a larger number of register marks, we can define the value of the register error as a statistical value rather than a single one. The register errors measured from an actual roll-to-roll printing system consist of a linearly varying term, a static offset term, and small fluctuations. The register errors resulting from the linearly varying term and the offset term are compensated for by the velocity and phase control of the plate cylinders, based on the calculated slope and offset of the register errors, which are obtained by the curve-fitting of the data set of register errors. We show that even with the slope and offset compensation of the register errors, a register control performance of within 20 µm can be achieved.