There is considerable covariation between externalizing and internalizing problems across the lifespan. Partitioning general and specific psychopathology is crucial to identify (a) processes that confer specific risk for externalizing versus internalizing problems and (b) transdiagnostic processes that confer risk for the covariation between externalizing and internalizing problems. The oddball P3 event-related potential (ERP) component, thought to reflect attentional orienting, has been widely examined in relation to psychopathology. However, prior studies have not examined the P3—or other aspects of neural functioning—in relation to general versus specific psychopathology in children. The present study examined whether children’s (N = 124, ages 3–7 years) P3 amplitudes were associated with general versus specific psychopathology. Children’s electroencephalography data were recorded during an oddball task. Parents rated their children’s externalizing and internalizing problems. Using bifactor models to partition variance in parents’ ratings of children’s psychopathology symptoms, we examined children’s P3 amplitudes in relation to three latent factors: (1) the general factor of psychopathology—the covariation of externalizing and internalizing psychopathology, (2) unique externalizing problems—the variance in externalizing problems after controlling for the general factor, and (3) unique internalizing problems. Results indicated that smaller P3 amplitudes were associated with unique externalizing problems at ages 3–5, and with general psychopathology at ages 6–7. Findings suggest that smaller P3 amplitudes may be associated with externalizing problems from a very young age. Moreover, there may be a developmental shift in the functional significance of the P3 in relation to general and specific psychopathology in childhood.