Extensive work implicates abnormal amygdala response during threatening stimuli in youth with antisocial behaviour. However, no research has examined whether youth identified in Primary and Secondary psychopathy subtypes would show differences in amygdala activity in response to threat acquisition and extinction. Latent profile analysis (LPA) was used to identify distinct antisocial groups based on participants’ scores on callous–unemotional (CU) traits, anxiety, and familial abuse in a sample of 136 high-risk adolescents (mean age = 17.7, SD = 1.6; 86% male). Functional MRI was then used to assess amygdala activation patterns during a classical differential delay threat-conditioning task. In addition to the Primary and Secondary subtypes, we identified groups mainly high on anxiety and others who were mainly high on abuse. Participants in the Primary group showed lower right amygdala activity in response to neutral male faces compared to the low, Anxious, and Secondary groups, whereas participants in the group with history of abuse exhibited higher right amygdala activity during threat acquisition compared to the rest of the groups. During threat extinction, the Primary group showed lower right amygdala activity compared to the Secondary and abuse groups. This is the first study to reveal amygdala activation in identified psychopathy-related variants during threat conditioning. We found that stratifying the sample based on the identified variants revealed amygdala functioning patterns that furthered our understanding of emotion-based deficits among high-risk adolescents.