Affective faces are important stimuli with relevance to healthy and abnormal social and affective information processing. The aim of this study was to investigate the effect of brief presentations of affective faces on attention and emotional state across the time course of stimulus processing, as indexed by startle eyeblink response modulation. Healthy adults were presented with happy, neutral, and disgusted male and female faces that were backward masked by neutral faces. Startle responses were elicited at 300, 800, and 3,500 ms following stimulus presentation to probe early and late startle eyeblink modulation, indicative of attention allocation and emotional state, respectively. Results revealed that, at 300 ms, both face expression and face gender modulated startle eyeblink response, suggesting that more attention was allocated to masked happy compared to disgusted female faces, and masked disgusted compared to neutral male faces. There were no effects of either face expression or face gender on startle modulation at 800 ms. At 3,500 ms, target face expression did not modulate startle, but male faces elicited larger startle responses than female faces, indicative of a more negative emotional state. These findings provide a systematic investigation of attention and emotion modulation by brief affective faces across the time course of stimulus processing.