A system includes an internal combustion engine, an exhaust conduit fluidly coupled to the internal combustion engine and an SCR catalyst, and a reductant doser operationally coupled to the exhaust conduit at a position upstream of the SCR catalyst. The reductant doser is responsive to a reductant doser command. The system includes a controller having a number of modules functionally structured to execute operations to compensate for transient operation of the system. An NH3 target module interprets a reductant amount target that is a target amount of reductant in the exhaust conduit at a position upstream of the SCR catalyst. A transient adjustment module detects a transient event in the SCR catalyst and provides an adjusted reductant amount target in response to the transient event and the reductant amount target. A dosing control module provides the reductant doser command in response to the adjusted reductant amount target.