Classical Pavlovian conditioning is a relatively simple behavioural experiment where a conditioned stimulus signals the occurrence of a reward. The repeated presentation of the stimulus and the reward leads to the evolution of a conditioned response. However, the electrophysiological correlates of participating brain structures, including the medial prefrontal cortex, that plays a role in decision making, and the central nucleus of the amygdala, that is responsible for reward learning and motivation, have not yet been fully explored. This study explores the electrophysiological properties of the prefrontal cortex and the amygdala in rats during Pavlovian conditioning, extinction and reacquisition. Multisite multichannel recordings showed a significant desynchronization in response to the conditioned stimulus. Additionally, the complex nature and role of a 4Hz activity and theta oscillation in both brain structures in reward conditioning was revealed. We found a consistent power and phase regulatory mechanism coordinating the 4Hz activity, while not affecting the theta oscillation, thus rendering these two distinct oscillations, with complementary roles, to fall out of synchrony. These findings might lay the foundations for further behavioural studies, mostly in the direction of social interaction and social behaviour.