The control of emissions from fossil-fired boilers wherein an injection of substances above the primary combustion zone employs multi-layer feedforward artificial neural networks for modeling static nonlinear relationships between the distribution of injected substances into the upper region of the furnace and the emissions exiting the furnace. Multivariable nonlinear constrained optimization algorithms use the mathematical expressions from the artificial neural networks to provide the optimal substance distribution that minimizes emission levels for a given total substance injection rate. Based upon the optimal operating conditions from the optimization algorithms, the incremental substance cost per unit of emissions reduction, and the open-market price per unit of emissions reduction, the intelligent emissions controller allows for the determination of whether it is more cost-effective to achieve additional increments in emission reduction through the injection of additional substance or through the purchase of emission credits on the open market. This is of particular interest to fossil-fired electrical power plant operators. The intelligent emission controller is particularly adapted for determining the economical control of such pollutants as oxides of nitrogen (NOx) and carbon monoxide (CO) emitted by fossil-fired boilers by the selective introduction of multiple inputs of substances (such as natural gas, ammonia, oil, water-oil emulsion, coal-water slurry and/or urea, and combinations of these substances) above the primary combustion zone of fossil-fired boilers.