Mechanisms of deep brain stimulation (DBS) on cortical networks were explored mainly by fMRI. Advanced analysis of high-density EEG is a source of additional information and may provide clinically useful biomarkers. The presented study evaluates EEG microstates in Parkinson's disease and the effect of DBS of the subthalamic nucleus (STN). The association between revealed spatiotemporal dynamics of brain networks and changes in oscillatory activity and clinical examination were assessed. Thirty-seven patients with Parkinson's disease treated by STN-DBS underwent two sessions (OFF and ON stimulation conditions) of resting-state EEG. EEG microstates were analyzed in patient recordings and in a matched healthy control dataset. Microstate parameters were then compared across groups and were correlated with clinical and neuropsychological scores. Of the five revealed microstates, two differed between Parkinson's disease patients and healthy controls. Another microstate differed between ON and OFF stimulation conditions in the patient group and restored parameters in the ON stimulation state toward to healthy values. The mean beta power of that microstate was the highest in patients during the OFF stimulation condition and the lowest in healthy controls; sources were localized mainly in the supplementary motor area. Changes in microstate parameters correlated with UPDRS and neuropsychological scores. Disease specific alterations in the spatiotemporal dynamics of large-scale brain networks can be described by EEG microstates. The approach can reveal changes reflecting the effect of DBS on PD motor symptoms as well as changes probably related to non-motor symptoms not influenced by DBS.