Differences in attentional orienting and regulation of arousal are frequently comorbid traits in many clinical populations including those with autism. The Arousal Biased Competition theory has shown that arousal strengthens pre-existing biases for the perception and memory of objects and may also influence the effectiveness of attentional orienting systems more generally. In order to investigate this possibility, 38 typically developing participants completed both pro- and antisaccade gap-overlap paradigms at multiple levels of autonomic arousal induced by varying levels of background noise and recorded using skin conduction level (SCL). Participants also completed the Autism Spectrum Quotient (AQ) and were assigned to either a high or low AQ group. Linear mixed effects modeling analysis showed several significant interactions between SCL and AQ with Task (prosaccade vs. antisaccade) and Trial Type (gap vs. overlap). We interpret these results as suggesting that arousal improves the effectiveness of top-down (endogenous) attentional mechanisms but notably this impact was weaker for individuals in the high AQ group. Thus, while arousal appears to play an important role in upregulating top-down control, this influence may be altered in autism.