Previous literature indicates that both hypoactivity and hyperactivity of the HPA axis may be related to conduct disorder and externalizing behaviors in young children. Using a longitudinal sample of 283 typically-developing children, the current study examined both the concurrent and the longitudinal association between HPA functioning and externalizing behavior problems, such as conduct problems. Diurnal cortisol rhythms and externalizing problems were assessed at ages 6 and 9. Results suggest that concurrent HPA functioning is not significantly related to externalizing behavior at ages 6 or 9. However, more blunted cortisol rhythms at age 6 (less change across the day from morning to evening) predicted a greater increase in externalizing behavior between age 6 and age 9 than did steeper cortisol rhythms. Further analyses revealed that this association was driven by conduct problems and aggressive behavior, rather than attention problems. The relationship between HPA functioning and subsequent externalizing behavior in children adds to the limited longitudinal work on this topic, suggesting that the association changes over time. These results may serve to clarify the inconsistencies in the cross-sectional literature, particularly with respect to young school-age children.