Narcolepsy is a chronic disorder of the sleep-wake cycle with pathological shifts between sleep stages. These abrupt shifts are induced by a sleep-regulating flip-flop mechanism which is destabilized in narcolepsy without obvious alterations in EEG oscillations. Here, we focus on the question whether the pathology of narcolepsy is reflected in EEG microstate patterns. 30 channel awake and NREM sleep EEGs of 12 narcoleptic patients and 32 healthy subjects were analyzed. Fitting back the dominant amplitude topography maps into the EEG led to a temporal sequence of maps. Mean microstate duration, ratio total time (RTT), global explained variance (GEV) and transition probability of each map were compared between both groups. Nine patients reached N1, 5 N2 and only 4 N3. All healthy subjects reached at least N2, 19 also N3. Four dominant maps could be found during wakefulness and all NREM- sleep stages in healthy subjects. During N3, narcolepsy patients showed an additional fifth map. The mean microstate duration was significantly shorter in narcoleptic patients than controls, most prominent in deep sleep. Single maps' GEV and RTT were also altered in narcolepsy. Being aware of the limitation of our low sample size, narcolepsy patients showed wake-like features during sleep as reflected in shorter microstate durations. These microstructural EEG alterations might reflect the intrusion of brain states characteristic of wakefulness into sleep and an instability of the sleep-regulating flip-flop mechanism resulting not only in pathological switches between REM- and NREM-sleep but also within NREM sleep itself, which may lead to a microstructural fragmentation of the EEG.