The dorsolateral prefrontal cortex (dlPFC) is thought to be a key site in the brain’s cognitive control network, supporting cognitive processes like attention and working memory [1–7]. There is also evidence that the dlPFC is engaged during anxiety regulation tasks, suggesting that anxiety regulation may be mediated in part by dlPFC activity [8–15]. However, the degree to which these two domains of processing overlap is unclear. Therefore, in the current study, we tested the hypothesis that the dlPFC regulates brain regions critical for the expression of anxiety. To do so, we used interleaved TMS/fMRI to record TMS-evoked BOLD responses during periods of threat compared to periods of safety. We hypothesized that TMS pulses would reduce activity in anxiety expression regions during threat. Forty-four healthy controls (no current or history of psychiatric disorders) were recruited to take part in a broader study. Participants completed the neutral, predictable, and unpredictable (NPU) threat task while receiving TMS pulses to either the right dlPFC or a control region. A whole brain analysis identified regions showing significant BOLD responses evoked by dlPFC stimulation. We then extracted these responses and compared those evoked during safe blocks to those evoked during unpredictable threat. We found that responses in the left insula (LI), right sensory/motor cortex (RSM), and a region encompassing the bilateral SMA regions (BSMA) showed significantly different responses during the safe blocks compare to the threat. During the safe periods, these regions showed significant BOLD deactivations. These deactivations were reduced during the threat blocks. Overall, these findings are largely consistent with the hypothesis that the dlPFC plays a role in the top-down control of emotion and suggest that dlPFC activity reduces downstream activity in emotional expression regions, but that this effect is reduced under threat.