Purpose <p>This study aims to evaluate the changes in the functional brain networks and graph theory analysis of patients with epilepsy and comorbid migraine without aura (EM).</p> Methods <p>We included 30 patients with EM, 20 healthy controls (HC) and 30 epilepsy controls (EC) without migraine. Resting-state functional magnetic resonance imaging was performed to obtain imaging data.</p> Results <p>The fractional amplitude of low-frequency fluctuations (fALFF) value of the left superior temporal gyrus was higher in the EM group than in the HC group. The regional homogeneity (ReHo) values of the right orbital superior frontal gyrus were higher in the EM group than in the EC group. The functional connectivity between left superior occipital gyrus and left orbital part of the superior frontal gyrus, left middle temporal gyrus, right orbital part of middle frontal gyruss, left medial superior frontal gyrus (cluster 2), right middle frontal gyrus, left middle frontal gyrus, left median cingulate and paracingulate gyri was enhanced in the EM group compared with the HC group; the functional connectivity between the left superior occipital and left medial superior frontal gyri (cluster 1) was weakened. The functional connectivity was weakened between the posterior default mode network (pDMN) and dorsal sensorimotor network (dSMN) and the left frontoparietal network (LFPN) and right frontoparietal network. The functional connectivity between pDMN and LFPN was enhanced in the EM group compared with the EC group. Graph theory analysis revealed that the area under the curve of the standardized characteristic path length of the EM group was smaller than that of the HC and EM groups.</p> Conclusion <p>The abnormal functional brain networks associated with pain regulation, and changes in topological properties may be involved in the mechanisms underlying migraine without aura occurrence in patients with epilepsy.</p>