Negative emotionality (NE) refers to individual differences in the propensity to experience and react with negative emotions and is associated with increased risk of psychological disorder. However, research on the neural bases of NE has focused almost exclusively on amygdala activity during emotional face processing. This study broadened this framework by examining the relationship between observed NE in early childhood and subsequent neural responses to emotional faces in both the amygdala and the fusiform face area (FFA) in a late childhood/early adolescent sample. Measures of NE were obtained from children at age 3 using laboratory observations, and functional magnetic resonance imaging (fMRI) data were collected when these children were between the ages of 9 and 12 while performing a visual stimulus identity matching task with houses and emotional faces as stimuli. Multiple regression analyses revealed that higher NE at age 3 is associated with significantly greater activation in the left amygdala and left FFA but lower functional connectivity between these two regions during the face conditions. These findings suggest that those with higher early NE have subsequent alterations in both activity and connectivity within an extended network during face processing.