We investigated the differences in functional connectivity based on the source-level electroencephalography (EEG) analysis between stroke patients with and without post-stroke epilepsy (PSE). Thirty stroke patients with PSE and 35 stroke patients without PSE were enrolled. EEG was conducted during a resting state period. We used a Brainstorm program for source estimation and the connectivity matrix. Data were processed according to EEG frequency bands. We used a BRAPH program to apply a graph theoretical analysis. In the beta band, radius and diameter were increased in patients with PSE than in those without PSE (2.699 vs. 2.579, adjusted p = 0.03; 2.261 vs. 2.171, adjusted p = 0.03). In the low gamma band, radius was increased in patients with PSE than in those without PSE (2.808 vs. 2.617, adjusted p = 0.03). In the high gamma band, the radius, diameter, average eccentricity, and characteristic path length were increased (1.828 vs. 1.559, adjusted p < 0.01; 2.653 vs. 2.306, adjusted p = 0.01; 2.212 vs. 1.913, adjusted p < 0.01; 1.425 vs. 1.286, adjusted p = 0.01), whereas average strength, mean clustering coefficient, and transitivity were decreased in patients with PSE than in those without PSE (49.955 vs. 55.055, adjusted p < 0.01; 0.727 vs. 0.810, adjusted p < 0.01; 1.091 vs. 1.215, adjusted p < 0.01). However, in the delta, theta, and alpha bands, none of the functional connectivity measures were different between groups. We demonstrated significant alterations of functional connectivity in patients with PSE, who have decreased segregation and integration in brain network, compared to those without PSE.