Adolescence is a period of heightened emotional reactivity, which is reflected in greater activation in emotion-processing regions of the brain in adolescents relative to children and adults. While elevated emotional reactivity and poor emotion regulation are thought to contribute to the rise in rates of internalizing psychopathology, including anxiety, during adolescence, little research has examined factors predicting individual differences in the neural regulation of emotion that can explain why only some adolescents experience anxiety. To address this gap, the present study examined the contribution of childhood negative emotionality (NE) and cognitive control (CC) to neural processing of emotion in adolescence. A sample of 44 girls (M age = 15.5, SD = 0.35) was selected from a longitudinal study that included self, parent, and teacher report of NE and CC between 2nd and 7th grades. Following 9th grade, girls completed an emotion regulation task during a functional magnetic resonance imaging scan. Neural regulation of emotion was indexed by functional connectivity between the amygdala and right ventrolateral prefrontal cortex (rVLPFC) during emotion regulation. Analyses revealed that NE predicted a less mature pattern of amygdala-rVLPFC connectivity while CC predicted a more mature pattern of amygdala-rVLPFC connectivity. Additionally, we found an interaction between NE and CC, such that NE predicted emotion dysregulation at low but not high levels of CC. Neural dysregulation of emotion was associated with anxiety symptoms across the following nine months. These findings identify important individual differences in the development of emotion dysregulation that contribute to risk for anxiety in adolescence.