The present disclosure relates to a method for controlling pressure of an engine, including a controller structured to implement the method and an engine system including the controller. More specifically, the present disclosure relates to a method based on a mass balance analysis of a fuel system to determine how much mass needs to be pumped to maintain or achieve a certain pressure for the engine. In some embodiments, the method analyzes how much mass can be pumped by each pumping event based on current engine conditions. The analysis is performed over the smallest repeatable pump events and cylinder events cycle, or “subcycle,” based on the number of pump events and cylinder events for a given engine configuration.