Widespread disturbances in resting state functional connectivity between remote brain areas have been demonstrated in patients with brain tumors. Functional connectivity has been associated with neurocognitive deficits in these patients. Thus far, it is unknown how (surgical) treatment affects functional connectivity. Functional connectivity before and after tumor resection was compared in primary brain tumor patients. Data from 15 newly diagnosed brain tumor patients were analyzed. Patients underwent tumor resection, and both preoperative (up to five months prior to surgery) and postoperative (up to ten months following surgery) resting state magnetoencephalography (MEG) recordings. Seven of the patients (47%) underwent radiotherapy after neurosurgery. Functional connectivity was assessed by the phase lag index (PLI), a measure of the correlation between MEG sensors that is not sensitive to volume conduction. PLIs were averaged to one short-distance and two long-distance (interhemispheric and intrahemispheric) scores in seven frequency bands. We found that functional connectivity changed in a complex manner after tumor resection, depending on frequency band and functional connectivity type. Post-hoc analyses yielded a significant decrease of interhemispheric PLI in the theta band after tumor resection. This result proved to be robust and was not influenced by radiotherapy or a variety of tumor- and patient-related factors.