Autism spectrum disorder (ASD) is highly comorbid with mood disorders, such as depression and anxiety. Previous research suggests difficulties in emotion regulation to be concordant with experiencing these comorbid symptoms. Understanding the neural correlates of emotion regulation in ASD and relationships with mood symptoms could provide insights for effective treatments. We employed an existing functional MRI paradigm to assess neural activation during an emotional regulation task in adults with ASD, and correlate activated regions with self-reported measures of depression and anxiety. We found the following regions to be significantly associated with emotion regulation (family-wise error corrected p<0.05): the bilateral insula, anterior cingulate, middle cingulate, precentral gyrus, angular gyrus, left dorsolateral PFC, right caudate/putamen, and left medial PFC. We found anxiety, but not depression, symptoms were negatively correlated with activation in the anterior cingulate, left insula, and left putamen, and showed a moderate relationship to the amygdala. These results expand current understanding of ASD and emotion regulation and suggest targets for future clinical intervention.