Abstract: The invention uses an input signal directly from a fuel flow device to control the amount of ammonia injected into a flue gas stream for NOx reduction for boilers. The control system receives a signal directly from a fuel flow device that indicates the amount of fuel flow and corresponding NOx emissions. The signal is processed using an algorithm with a multi-loop controller and an ammonia mass flow control valve with temperature and pressure corrections to determine how much ammonia must be injected into the flue gas in the presence of a catalyst to achieve the desired NOx emissions reductions. A dilution air blower transports ammonia to an injection grid and subsequently, the ammonia reacts with the flue gas in the presence of a catalyst to reduce the amount of NOx emissions to the desired level.