In the organizing of professional training, the assessment of the trainee’s reaction and state in stressful situations is of great importance. Phobic reactions are a specific type of stress reaction that, however, is rarely taken into account when developing virtual simulators, and are a risk factor in the workplace. A method for evaluating the impact of various phobic stimuli on the quality of training is considered, which takes into account the time, accuracy, and speed of performing professional tasks, as well as the characteristics of electroencephalograms (the amplitude, power, coherence, Hurst exponent, and degree of interhemispheric asymmetry). To evaluate the impact of phobias during experimental research, participants in the experimental group performed exercises in different environments: under normal conditions and under the influence of acrophobic and arachnophobic stimuli. The participants were divided into subgroups using clustering algorithms and an expert neurologist. After that, a comparison of the subgroup metrics was carried out. The research conducted makes it possible to partially confirm our hypotheses about the negative impact of phobic effects on some participants in the experimental group. The relationship between the reaction to a phobia and the characteristics of brain activity was revealed, and the characteristics of the electroencephalogram signal were considered as the metrics for detecting a phobic reaction.