A method and system for controlling the fuel mass to be delivered to an individual cylinder of an internal combustion engine during engine transients caused by intake control device transitions. The method and system compensates for fuel transport dynamics and the actual fuel injected into the cylinder. A plurality of engine parameters are sensed, including cylinder air charge. An initial base desired fuel mass is determined based on the plurality of engine parameters. An initial transient fuel mass is also determined based on prior injection history which, in turn, is modified based on the transition of the intake control device for that cylinder. A desired injected fuel mass to be delivered to the cylinder is determined based on the initial base desired fuel mass and the initial transient fuel mass. These same calculations are then used to compensate for changes to the base desired fuel mass while the fuel injection is in progress, resulting in an updated desired injected fuel mass. Finally, the injection history for that cylinder is updated to account for the actual desired fuel mass delivered to the cylinder.