Travel time, or, more generally, level of service, has always been considered the main parameter with which to design roads, particularly in extra-urban areas where geometries and policies, such as speed limits, play a key role in the performance achieved. Unfortunately, this type of approach does not consider the impact on emissions that is obtained when only performance-based goals are pursued. The paper deals with the analysis of the impact on emissions and fuel consumption under different traffic conditions, and we present a new methodology for emission estimation based on the stochastic formulation of the fundamental diagram in a highway environment. The proposed methodology estimates the emissions using a stochastic adaptation of the CORINAIR methodology based on COPERT software on both specific vehicle types and the average Italian vehicle fleet. As expected, due to the convexity of the emission function, accounting for speed dispersion leads to an increase in energy consumption and emissions. Tests show that the stochastic component can lead to an increase in the emission estimation up to 5.5% and, therefore, it should be considered. The methodology has been applied by means of real trajectories, and the results of the application show that performance optimization strategies can contrast with sustainability and emission reduction policies. Results show that for some vehicular classes, emissions or fuel consumption are highly dependent on speed, with different proportionalities. In all cases, the minimum consumption is obtained at speeds ranging from 70 to 90 km/h. The analysis of the curves shows that an increase in speeds, even to reach low speeds, generally leads to an increase in energy consumption and emissions per kilometer traveled and, therefore, is independent of the decrease in travel time.