Background: Self-agency (SA) is a person's feeling that his action was generated by himself. The neural substrates of SA have been investigated in many neuroimaging studies, but the functional connectivity of identified regions has rarely been investigated. The goal of this study is to investigate the neural network related to SA. Methods: SA of hand movements was modulated with virtual reality. We examined the cortical network relating to SA modulation with electroencephalography (EEG) power spectrum and phase coherence of alpha, beta, and gamma frequency bands in 16 right-handed, healthy volunteers. Results: In the alpha band, significant relative power changes and phase coherence of alpha band were associated with SA modulation. The relative power decrease over the central, bilateral parietal, and right temporal regions (C4, Pz, P3, P4, T6) became larger as participants more effectively controlled the virtual hand movements. The phase coherence of the alpha band within frontal areas (F7-FP2, F7-Fz) was directly related to changes in SA. The functional connectivity was lower as the participants felt that they could control their virtual hand. In the other frequency bands, significant phase coherences were observed in the frontal (or central) to parietal, temporal, and occipital regions during SA modulation (Fz-O1, F3-O1, Cz-O1, C3-T4L in beta band; FP1-T6, FP1-O2, F7-T4L, F8-Cz in gamma band). Conclusions: Our study suggests that alpha band activity may be the main neural oscillation of SA, which suggests that the neural network within the anterior frontal area may be important in the generation of SA.