Associative learning forms when there is temporal relationship between a stimulus and a reinforcer, yet the inter-trial-interval (ITI), which is usually much longer than the stimulus-reinforcer-interval, contributes to learning-rate and memory strength. The neural mechanisms that enable maintenance of time between trials remain unknown, and it is unclear if the amygdala can support time scales at the order of dozens of seconds. We show that the ITI indeed modulates rate and strength of aversive-learning, and that single-units in the primate amygdala and dorsal-anterior-cingulate-cortex signal confined periods within the ITI, strengthen this coding during acquisition of aversive-associations, and diminish during extinction. Additionally, pairs of amygdala-cingulate neurons synchronize during specific periods suggesting a shared circuit that maintains the long temporal gap. The results extend the known roles of this circuit and suggest a mechanism that maintains trial-structure and temporal-contingencies for learning.