The electroencephalogram (EEG) of patients suffering from inflammatory diseases of the brain may show specific waveforms called slow biphasic complexes (SBC). Recent studies indicated a correlation between the severity of encephalitis and some features of SBCs, such as location, amplitude and frequency of appearance. Moreover, EEG rhythms were found to vary before the onset of an SBC, as if the brain was preparing to the discharge (actually with a slowing down of the EEG oscillation). Here, we investigate possible variations of EEG functional connectivity (FC) in EEGs from pediatric patients with different levels of severity of encephalitis. FC was measured by the maximal crosscorrelation of EEG rhythms in different bipolar channels. Then, the indexes of network patterns (namely strength, clustering coefficient, efficiency and characteristic path length) were estimated to characterize the global behavior when they are measured during SBCs or far from them. EEG traces showed statistical differences in the two conditions: clustering coefficient, efficiency and strength are higher close to an SBC, whereas the characteristic path length is lower. Moreover, for more severe conditions, an increase in clustering coefficient, efficiency and strength and a decrease in characteristic path length were observed in the delta–theta band. These outcomes support the hypothesis that SBCs result from the anomalous coordination of neurons in different brain areas affected by the inflammation process and indicate FC as an additional key for interpreting the EEG in encephalitis patients.