Attention-deficit/hyperactivity disorder (ADHD) and bipolar disorder (BD) are highly comorbid and share executive function and emotion processing deficits, complicating diagnoses despite distinct clinical features. We compared performance on an oculomotor task that assessed these processes to capture subtle differences between ADHD and BD. The interaction between emotion processing and executive functioning may be informative because, although these processes overlap anatomically, certain regions that are compromised in each network are different in ADHD and BD. Adults, aged 18–62, with ADHD (n = 22), BD (n = 20), and healthy controls (n = 21) performed an interleaved pro- and antisaccade task (looking toward vs. looking away from a visual target, respectively). Task irrelevant emotional faces (fear, happy, sad, neutral) were presented on a subset of trials either before or with the target. The ADHD group made more direction errors (looked in the wrong direction) than controls. Presentation of negatively valenced (fear, sad) and ambiguous (neutral) emotional faces increased saccadic reaction time in BD only compared to controls, whereas longer presentation of sad faces modestly increased group differences. The antisaccade task differentiated ADHD from controls. Emotional processing further impaired processing speed in BD. We propose that the dorsolateral prefrontal cortex is critical in both processing systems, but the inhibitory signal this region generates is impacted by dysfunction in the emotion processing network, possibly at the orbitofrontal cortex, in BD. These results suggest there are differences in how emotion processing and executive functioning interact, which could be utilized to improve diagnostic specificity.