A control system for an engine having a first cylinder and a second cylinder is disclosed having a first engine valve movable to regulate a fluid flow of the first cylinder and a first actuator associated with the first engine valve. The control system also has a second engine valve movable to regulate a fluid flow of the second cylinder and a sensor configured to generate a signal indicative of a pressure within the first cylinder. The control system also has a controller that is in communication with the first actuator and the sensor. The controller is configured to compare the pressure within the first cylinder with a desired pressure and selectively regulate the first actuator to adjust a timing of the first engine valve independently of the timing of the second engine valve based on the comparison.