Functional magnetic resonance imaging (fMRI) studies of conduct disorder (CD) have mostly been limited to males. Here, we examined whether male and female youth with CD showed similar or distinct alterations in brain responses to emotional faces, using a large, mixed-sex sample of youths with CD. We also investigated the influence of callous-unemotional (CU) traits. Brain responses to angry, fearful, and neutral faces were assessed in 161 CD youths (74 females) and 241 typically-developing (TD) youths (139 females) aged 9-18 years. Categorical analyses tested for diagnosis effects (CD vs. TD and CD with high [CD/HCU] vs. low [CD/LCU] levels of CU traits vs. TD) and sex-by-diagnosis interactions. When processing faces in general (all faces versus baseline), youths with CD exhibited lower amygdala responses compared to TD youths, which appeared driven by the CD/HCU subgroup. Sex-by-CU subgroups interactions were identified in the amygdala (CD/LCU females<TD females; CD/LCU males>TD males) and insula (CD/HCU females>CD/LCU females; CD/HCU males<CD/LCU males). The findings for males support an influential neurocognitive model of CD. However, the association between CU traits and brain response to facial expressions differed in females and males with CD, suggesting distinct pathophysiological processes.