<p>Callous-unemotional traits are a major risk factor for aggression and other externalizing behaviors. These traits frequently co-occur with maltreatment exposure, and both of these variables have been independently linked to changes in amygdala structure and function. However, relatively little research has explored how trauma exposure and amygdala structure and function combine to shape callous-unemotional traits. We assessed maltreatment exposure and callous-unemotional traits at two timepoints in children and adolescents who were aged 8–16 years at baseline (54.37% Male, 45.63% Female). We also used magnetic resonance imaging (MRI) to assess amygdala volume and activation in a subset of these youths at baseline (<i>N</i> = 161) and 18 months later (N <b>=</b> 117) using both linear and non-linear approaches. At baseline, maltreatment exposure and callous-unemotional traits were both independently associated with reduced right and left amygdala volume. Callous-unemotional traits, but not maltreatment exposure, were also associated with reduced activation in right amygdala. Lower amygdala volume at baseline and maltreatment exposure independently predicted increases in callous-unemotional traits 18 months later. However, the effect of maltreatment on callous-unemotional traits was not mediated by amygdala volume. We find that accounting for maltreatment and amygdala volume, but not amygdala activation, improves the prediction of future callous-unemotional trait severity. These findings provide the first longitudinal evidence that maltreatment and lower amygdala volume independently predict worsening callous-unemotional traits in high-risk youths.</p>