People with epilepsy often suffer from comorbid psychiatric disorders, which negatively affects their quality of life. Emotion regulation is an important cognitive process that is impaired in individuals with psychiatric disorders, such as depression. Adults with epilepsy also show difficulties in emotion regulation, particularly during later-stage, higher-order cognitive processing. Yet, the spatiotemporal and frequency correlates of these functional brain deficits in epilepsy remain unknown, as do the nature of these deficits in adolescent epilepsy. Here, we aim to elucidate the spatiotemporal profile of emotional conflict processing in adolescents with epilepsy, relative to controls, using magnetoencephalography (MEG) and relate these findings to anxiety and depression symptom severity assessed with self-report scales. We hypothesized to see blunted brain activity during emotional conflict in adolescents with epilepsy, relative to controls, in the posterior parietal, prefrontal and cingulate cortices due to their role in explicit and implicit regulation around participant response (500-1000 ms). We analyzed MEG recordings from 53 adolescents (28 epilepsy [14focal,14generalized], 25 controls) during an emotional conflict task. We showed that while controls exhibited behavioral interference to emotional conflict, adolescents with epilepsy failed to exhibit this normative response time pattern. Adolescents with epilepsy showed blunted brain responses to emotional conflict in brain regions related to error evaluation and learning around the average response time (500-700 ms), and in regions involved in decision making during post-response monitoring (800-1000 ms). Interestingly, behavioral patterns and psychiatric symptom severity varied between epilepsy subgroups, wherein those with focal epilepsy showed preserved response time interference. Thus, brain responses were regressed with depression and anxiety levels for each epilepsy subgroup separately. Analyses revealed that under activation in error evaluation regions (500-600 ms) predicted anxiety and depression in focal epilepsy, while regions related to learning (600-700 ms) predicted anxiety in generalized epilepsy, suggesting differential mechanisms of dysfunction in these subgroups. Despite similar rates of anxiety and depression across the groups, adolescents with epilepsy still exhibited deficits in emotional conflict processing in brain and behavioral responses. This suggests that these deficits may exist independently from psychopathology and may stem from underlying dysfunctions that predispose these individuals to develop both disorders. Findings such as these may provide potential targets for future research and therapies.