The constant interplay between affective processing and cognitive control supports emotion regulation and appropriate social functioning. Even when affective stimuli are processed implicitly, threat-related stimuli are prioritized in the earliest stages of processing; yet, it remains unclear how implicit attention to affect influences subsequent cognitive control functions. The present study evaluated the influence of affective valence on early perceptual processes and subsequent response inhibition in a context where affective properties of the stimuli (facial expressions) were not critical for performing the task. Participants (N = 32) completed an affective stop-signal task (SST) while their scalp EEGs were recorded. The SST assessed response inhibition while participants implicitly attended to happy and afraid facial expressions that were matched for level of arousal. Behavioral performance was measured via response time and accuracy while physiological response was measured via the P100, N170, and N200/P300 ERP components. Decreased gender discrimination accuracy, delayed P100 latency, and more negative N170 amplitude were observed for afraid faces compared to happy faces, suggesting a shift in processing with respect to face valence. However, differences in stopping accuracy or N200/P300 ERP components during response inhibition were not observed, pointing to top-down cognitive processes likely being recruited to override the early automatic response to prioritize threat-related stimuli. Findings highlight that, in this implicit affective attention task, threat-related stimuli are prioritized early during processing, but implicitly attending to differentially valenced stimuli did not modulate subsequent cognitive control functions.