A system and method for controlling the clutches in a vehicle powershift transmission. The control system includes a microprocessor which periodically executes an algorithm and which has a memory in which is stored a sequential set of time reference values and a sequential set of pressure values. The control system applies to each oncoming element a fill pressure pulse for fill periods which are unique for each element. The control system determines shift time values, subsequent to filling of the control elements, as a function of the fill period. The control system applies pressure signals to the control elements at times represented by the shift time values which are unique for each element. The control system determines, subsequent to a realignment time, realignment shift time values which are the same for all of the control elements. The control system also applies pressure signals to the control elements subsequent to the realignment time, at times determined as a function of the realignment shift time values.