Neuroscientists are becoming interested in the application of computational EEG analysis to the identification of ictal onset zones, however, most studies have focused on the localization of ictal onset zones in focal epilepsy. The present study aimed to estimate the ictal onset zone of Lennox-Gastaut syndrome (LGS) with bilaterally synchronous epileptiform discharges from intracranial electroencephalography (iEEG) recordings using directional connectivity analysis. We analyzed ictal iEEG data acquired from three patients with LGS. To identify the ictal onset zones, we estimated the functional directional connectivity network among the intracerebral electrodes using the directed transfer function (DTF) method. The analysis results demonstrated that areas with high average outflow values corresponded well with the surgical resection areas identified using electrophysiologic data and conventional neuroimaging modalities. Our results suggest that the DTF analysis can be a useful auxiliary tool for determining surgical resection areas prior to epilepsy surgery in LGS patients.