Methods and systems are provided related to an emissions control system. The emissions control system has an exhaust after-treatment system defining a plurality of distinct exhaust flow passages through which at least a portion of an exhaust stream can flow, e.g., the exhaust stream is produced by an engine. The emissions control system also includes a controller for controlling injection of reductant into the exhaust stream flowing through each of the flow passages. In one example, the emissions control system is configured for use in a vehicle, such as a locomotive or other rail vehicle.