Survival in natural environments for small animals such as rats often depends upon precise neural coding of life-threatening acoustic signals, and binaural unmasking of species-specific pain calls is especially critical. This study investigated how species-specific tail-pain chatter is represented in the rat amygdala, which receives afferents from both auditory thalamus and auditory association cortex, and whether the amygdaloid representation of the chatter can be binaurally unmasked. The results show that chatter with a fundamental frequency (F0) of 2.1 kHz was able to elicit salient phase-locked frequency-following responses (FFRs) in the lateral amygdala nucleus in anesthetized rats. FFRs to the F0 of binaurally presented chatter were sensitive to the interaural time difference (ITD), with the preference of ipsilateral-ear leading, as well as showing features of binaural inhibition. When interaurally correlated masking noises were added and ipsilateral chatter led contralateral chatter, introducing an ITD disparity between the chatter and masker significantly enhanced (unmasked) the FFRs. This binaural unmasking was further enhanced by chemically blocking excitatory glutamate receptors in the auditory association cortex. When the chatter was replaced by a harmonic tone complex with an F0 of 0.7 kHz, both the binaural-inhibition feature and the binaural unmasking were preserved only for the harmonic of 2.1 kHz but not the tone F0. These results suggest that both frequency-dependent ascending binaural modulations and cortical descending modulations of the precise auditory coding of the chatter in the amygdala are critical for processing life-threatening acoustic signals in noisy, and even reverberant environments.