Occupational noise frequently occurs in the work environment in military intelligence, surveillance, and reconnaissance operations. This impacts cognitive performance by acting as a stressor, potentially interfering with the analysts’ decision-making process. We investigated the effects of different noise stimuli on analysts’ performance and workload in anomaly detection by simulating a noisy work environment. We utilized functional near-infrared spectroscopy (fNIRS) to quantify oxy-hemoglobin (HbO) and deoxy-hemoglobin concentration changes in the prefrontal cortex (PFC), as well as behavioral measures, which include eye tracking, reaction time, and accuracy rate. We hypothesized that noisy environments would have a negative effect on the participant in terms of anomaly detection performance due to the increase in workload, which would be reflected by an increase in PFC activity. We found that HbO for some of the channels analyzed were significantly different across noise types ( p < 0.05 ). Our results also indicated that HbO activation for short-intermittent noise stimuli was greater in the PFC compared to long-intermittent noises. These approaches using fNIRS in conjunction with an understanding of the impact on human analysts in anomaly detection could potentially lead to better performance by optimizing work environments.