Disclosed are model predictive control (MPC) systems, methods for using such MPC systems, and motor vehicles with selective catalytic reduction (SCR) employing MPC control. An SCR-regulating MPC control system is disclosed that includes an NOx sensor for detecting nitrogen oxide (NOx) input received by the SCR system, catalyst NOx sensors for detecting NOx output for two SCR catalysts, and catalyst NH3 sensors for detecting ammonia (NH3) slip for each SCR catalyst. The MPC system also includes a control unit programmed to: receive desired can conversion efficiencies for the SCR catalysts; determine desired can NOx outputs for the SCR catalysts; determine maximum NH3 storage capacities for the SCR catalyst; calculate the current can conversion efficiency for each SCR catalyst; calculate an optimized reductant pulse-width and/or volume from the current can conversion efficiencies; and, command an SCR dosing injector to inject a reductant into an SCR conduit based on the calculated pulse-width/volume.