In this paper, we propose optimal route guidance and Nonlinear Model Predictive Control (NMPC)-based gating control approach to reduce network-wide emission in an urban traffic network. An accumulation-based Macroscopic Fundamental Diagram (MFD) model of a single region city is developed to describe the evaluation of the traffic flows in a network. Moreover, a path flow distribution scheme using Dynamic User Equilibrium (DUE) discipline is designed to reproduce the driver's adaptation to controlled flow. The NMPC is developed to track the optimal green routing coefficients which will indirectly track the network-wide emission levels by manipulating the traffic flows into a region. Simulation results show the effectiveness of the proposed scheme in improving the traffic emissions inside and outside the perimeter. Comparative analysis of no control and NMPC shows that the proposed approach reduces emission by up to 13% as compared to the no control case.