Animals can remember a situation associated with an aversive event. Contextual fear memory is initially encoded and consolidated in the hippocampus and gradually consolidated in multiple brain regions over time, including the medial prefrontal cortex (PFC). However, it is not fully understood how PFC neurons contribute to contextual fear memory formation during learning. In the present study, neuronal activity was increased in PFC neurons utilizing the pharmacogenetic hM3Dq-system in male mice. We show that fear expression and memory formation are enhanced by increasing neuronal activity in PFC during conditioning phase. Previous studies showed that the activation of hM3Dq receptor in a subset of amygdala neurons enhanced fear memory formation and biased which neurons are allocated to a memory trace, in which immediate early gene c-fos was preferentially expressed following memory retrieval in these pre-activated neurons. In this study, hM3Dq activation in PFC could not change the probability of c-fos expression in pre-activated neurons flowing memory retrieval. Instead, the number c-fos positive neurons following memory retrieval was significantly increased in the basolateral amygdala. Our results suggest that neuronal activity in PFC at the time of learning modulates fear memory formation and downstream cellular activity at an early phase.