Radiation therapy plays a crucial role in the treatment of tumors of the central nervous system. However, along with the therapeutic effect, the exposure predetermines a wide variability in the manifestations of functional reactions, causing various cerebrovascular damage and hemodynamic changes without deteriorating the organism’s capabilities under adequate functional loads. In clinical practice, attention is directed to the problem of diagnosing the side effects of treatment in patients with cerebral tumors using modern neuroimaging methods. Over the past few years, there has been an increase in the number of researchers using functional near-infrared spectroscopy. However, there is still a problem of the lack of a generally accepted method for signal isolation and processing, which makes it difficult to compare the results of researches by different authors. In this article, the methodological part was developed and introduced into clinical research. Interhemispheric changes in the hemodynamic parameters of the brain in the frontotemporal region were reviewed in patients undergoing radiation therapy. The research was carried out in a resting state for 5 min. It was revealed that with right-sided radiation exposure, there is widespread weakening and reduction of intrahemispheric and interhemispheric functional connectivity. With left-sided radiation exposure, preservation of left-sided intrahemispheric connections and an increase in negative connections with the right hemisphere were observed. The analysis of resting-state functional connectivity using fNIRS may be a promising method for studying various pathological conditions, including the effects of ionizing exposure.