Background and Purpose We aimed to reveal resting-state functional connectivity characteristics based on the spike-free waking electroencephalogram (EEG) of benign epilepsy with centrotemporal spikes (BECTS) patients, which usually appears normal in routine visual inspection. Methods Thirty BECTS patients and 30 disease-free and age- and sex-matched controls were included. Eight-second EEG epochs without artifacts were sampled and then bandpass filtered into the delta, theta, lower alpha, upper alpha, and beta bands to construct the association matrix. The weighted phase lag index (wPLI) was used as an association measure for EEG signals. The band-specific connectivity, which was represented as a matrix of wPLI values of all edges, was compared for analyzing the connectivity itself. The global wPLI, characteristic path length (CPL), and mean clustering coefficient were compared. Results The resting-state functional connectivity itself and the network topology differed in the BECTS patients. For the lower-alpha-band and beta-band connectivity, edges that showed significant differences had consistently lower wPLI values compared to the disease-free controls. The global wPLI value was significantly lower for BECTS patients than for the controls in lower-alpha-band connectivity (mean±SD; 0.241±0.034 vs. 0.276±0.054, p =0.024), while the CPL was significantly longer for BECTS in the same frequency band (mean±SD; 4.379±0.574 vs. 3.904±0.695, p =0.04). The resting-state functional connectivity of BECTS showed decreased connectivity, integration, and efficiency compared to controls. Conclusions The connectivity differed significantly between BECTS patients and disease-free controls. In BECTS, global connectivity was significantly decreased and the resting-state functional connectivity showed lower efficiency in the lower alpha band.