Growing evidence indicates that anxiety impairs cognitive control processes, including inhibitory functioning. However, there are reports of anxiety state-related improvements in response inhibition performance in a go/nogo (GNG) task. Here we employed the stop-signal task (SST) to examine in complementary fashion the link between anticipatory anxiety and inhibitory control. Participants (N = 45) completed the SST under threat of unpredictable shocks and safe conditions while physiological activity (skin conductance and heart rate) was monitored. In addition to increased physiological activity, we found that stop-signal reaction time (SSRT), a robust measure of stopping efficiency, was prolonged during threat compared to safe without any difference in choice reaction times to go stimuli. This finding supports the claim of impaired inhibitory control in anxiety, and by consideration of differences between the SST and GNG tasks, can be reconciled with evidence of improved response inhibition on the latter under similar threat conditions.