Lesion studies show that goal-directed actions mediated by action-outcome (A-O) associations and habits mediated by stimulus-response (S-R) associations can be dissociated during instrumental training, with the prelimbic region of the medial prefrontal cortex being involved in the former and the infralimbic region in the latter. The present work further investigates the role of the prelimbic region in acquisition vs. expression of goal-directed instrumental behaviour, using reversible neuronal inactivation and outcome devaluation procedures. In a first experiment, inactivating the prelimbic cortex at the time of testing did not alter the sensitivity to devaluation, indicating that this region was not essential for the expression of A-O associations. In a second experiment, the prelimbic cortex was inactivated throughout the training phase. At the time of testing the performance was insensitive to devaluation, indicating that the acquired response was not goal-directed but mediated by an S-R association. These data challenge the view that the habit system replaces the goal-directed system as training progresses. They show that the prelimbic cortex plays a transient but crucial role in the acquisition of goal-directed responding and that the A-O and S-R systems can operate in a competitive fashion early in training.