Abnormalities in reward and punishment processing are implicated in the development of conduct problems (CP), particularly among youth with callous-unemotional (CU) traits. However, no studies have examined whether CP children with high versus low CU traits exhibit differences in the neural response to reward and punishment. A clinic-referred sample of CP boys with high versus low CU traits (ages 8–11; n = 37) and healthy controls (HC; n = 27) completed a fMRI task assessing reward and punishment processing. CP boys also completed a randomized control trial examining the effectiveness of an empirically-supported intervention (i.e., Stop-Now-And-Plan; SNAP). Primary analyses examined pre-treatment differences in neural activation to reward and punishment, and exploratory analyses assessed whether these differences predicted treatment outcome. Results demonstrated associations between CP and reduced amygdala activation to punishment independent of age, race, IQ and co-occurring ADHD and internalizing symptoms. CU traits were not associated with reward or punishment processing after accounting for covariates and no differences were found between CP boys with high versus low CU traits. While boys assigned to SNAP showed a greater reduction in CP, differences in neural activation were not associated with treatment response. Findings suggest that reduced sensitivity to punishment is associated with early-onset CP in boys regardless of the level of CU traits.