A method of handling a first random access procedure on a Primary Cell (PCell) for a mobile device when a second random access procedure on a Secondary Cell (SCell) is ongoing or is about to start is disclosed. The method comprises selectively initiating the first random access procedure on the PCell according to a result of the second random access procedure after the mobile device completes the second random access procedure on the SCell, wherein the first random access procedure is triggered by a pending scheduling request of the mobile device and the second random access procedure is triggered by need of synchronization on the SCell.