Background: Repetitive transcranial magnetic stimulation (rTMS) is one of high-potential non-pharmacological methods for migraine treatment. The purpose of this study is to objectively evaluate the efficacy of rTMS in patients with migraine based on data from functional magnetic resonance imaging (fMRI). Methods: 19 patients with migraine without aura underwent a 5-day course of rTMS of the ventrolateral prefrontal cortex bilaterally, at 10Hz frequency and 60% of motor threshold response of 900 pulses. Resting-state functional MRI (1.5 T) and battery of tests were carried out for each patient to clarify their diagnosis, qualitative and quantitative characteristics of pain, and associated affective symptoms. Changes in functional connectivity (FC) in the brain’s neural networks before and after the treatment were identified through independent components analysis. Results: Over the course of therapy, we observed an increase in FC of the default mode network within it, with pain system components and with structures of the visual network. We also noted a decrease in FC of the salience network with sensorimotor and visual networks, as well as an increase in FC of the visual network. Besides, we identified 5 patients who did not have a positive response to one rTMS course, presumably because of an increased trend to depressive symptoms and neuroimaging criteria for depressive disorder. Conclusions: Our findings provide evidence of a 70% efficacy of rTMS judging by neuroimaging changes and a decrease in clinical symptoms. Moreover, we identified neuroimaging criteria for the therapy efficacy as well as possible predictors of successful/unsuccessful response to the therapy.