Migraine is a common disorder with high social and medical impact. Patients with migraine have a much higher chance of experiencing headache attacks compared with the general population. Recent neuroimaging studies have confirmed that pathophysiology in the brain is not only limited to the moment of the attack but is also present in between attacks, the interictal phase. In this study, we hypothesized that the topology of functional brain networks is also different in the interictal state, compared with people who are not affected by migraine. We also expected that the level of network disturbances scales with the number of years people have suffered from migraine. Functional connectivity between 78 cortical brain regions was estimated for source-level magnetoencephalography data by calculating the phase lag index, in five frequency bands (delta-beta), and compared between healthy controls (n = 24) and patients who had been suffering from migraine for longer than 6 years (n = 12) or shorter than 6 years (n = 12). Moreover, the topology of the functional networks was characterized using the minimum spanning tree. The migraine groups did not differ from each other in functional connectivity. However, the network topology was different compared with healthy controls. The results were frequency specific, and higher average nodal betweenness centrality was specifically evident in higher frequency bands in patients with longer disease duration, while an opposite trend was present for lower frequencies. This study shows that patients with migraine have a different network topology in the resting state compared with healthy controls, whereby specific brain areas have altered topological roles in a frequency-specific manner. Some alterations appear specifically in patients with long-term migraine, which might show the long-term effects of the disease.