When we decide between two options, we can make our decision based on what we prefer, (preference-based choice), or we can also choose based on which option we want to avoid more (non-preference-based choice). Most decision making research has examined preference-based choice but has not differentiated it from non-preference-based choice. The decision making process can be decomposed into multiple value-based computational processes, which are shown to be subserved by different regions in the prefrontal cortex (PFC). Here we show that the same decision circuits within the PFC are configured differently depending on whether decisions are made based on preference or non-preference criteria (decision rule). Activation in the dorsolateral PFC changed depending on both the values of the two choice options and decision rule. We also found that activation in the medial and lateral PFC was modulated linearly according to the difference in value between the two items and according to the value of the chosen item, respectively. In the medial and lateral PFC, there were distinct patterns of activation between dorsal and ventral regions: in dorsal regions value-related changes in activation were modulated by the decision rule, whereas in ventral regions activation patterns were not modulated. We propose that preference and non-preference decision rules represented in the dorsal PFC differently configure decision processes, resulting in context-specific significance being attached to the choice values represented in the ventral PFC.