Development of computationally fast, numerically robust, and physically accurate models to compute engine-out emissions can play an important role in the design, development, and optimization of automotive engines powered by alternative fuels (such as natural gas and H2) and fuel blends (such as ethanol-blended fuels and biodiesel-blended fuels). Detailed multidimensional models that couple fluid dynamics and chemical kinetics place stringent demands on the computational resources and time, precluding their use in design and parametric studies. This work describes the development of an integrated design tool that couples a fast, robust, physics-based, two-zone quasi-dimensional engine model with modified reaction-rate-controlled models to compute engine-out NO and CO for a wide variety of fuel-additive blends. This integrated tool was designed to evaluate engine performance and emissions on the order of a typical engine cycle (∼25 -50 milliseconds) to enable its use for real-time control and optimization.As an illustrative example, this tool was used to study the engine-out NO and CO in a natural gas engine. The engine-out CO and NO predicted by the model showed good agreement with experimental data. The performance and emission computations for a single engine cycle were completed in about 8 milliseconds.