Affinity-purified antibody to S100 calcium binding protein B that has undergone gradual technological processing and was additionally modified with an electromagnetic signal is an active pharmaceutical substance of a novel drug Prospekta. Earlier studies have shown that the drug possesses a wide range of pharmacological properties, not limited to pro-cognitive and anxiolytic activity. Here, we aimed to determine the effect of Prospekta on the baseline electrical activity of the mouse brain. Extradural electrodes were surgically implanted into the skull of adult male socially submissive mice. Mice were orally administered Prospekta or purified water as a control via gavage for 5 days starting from the end of the recovery period. Brain baseline activity was recorded during 5 min after placing animals into arena. Quantitative measures of EEG delta (1–4 Hz), theta (4–8 Hz), alpha (8–13 Hz), beta (13–30 Hz), and gamma (30–100 Hz) power were assessed. It was shown that the drug led to a decrease in theta and alpha band power in the left prefrontal cortex. Furthermore, the drug exhibited a tendency to influence the coherence of electrical activity between the left prefrontal cortex and the right hippocampus, resulting in a moderate phase shift across all examined brain regions. At the same time, no prominent changes in EEG activity were observed in the right hippocampal region. We show that Prospekta modifies EEG parameters of animals and thereby confirm that the drug mechanism of action is based on its ability to affect functional (electrophysiological) brain activity.