Besides gelastic seizures, hypothalamic hamartoma (HH) is also noted for its susceptibility to remote secondary epileptogenesis. Although clinical observations have demonstrated its existence, and a three-stage theory has been proposed, how to determine whether a remote symptom is spontaneous or dependent on epileptic activities of HH is difficult in some cases. Herein, we report a case of new non-gelastic seizures in a 9-year-old female associated with a postoperatively remaining HH. Electrophysiological examinations and stereo-electroencephalography (SEEG) demonstrated seizure onsets with slow-wave and fast activities on the outside of the HH. By using computational methodologies to calculate the network dynamic effective connectivities, the importance of HH in the epileptic network was revealed. After SEEG-guided thermal coagulation of the remaining HH, the patient finally was seizure-free at the 2-year follow-up. This case showed the ability of computational methods to reveal information underlying complex SEEG signals, and further demonstrated the dependent-stage secondary epileptogenesis, which has been rarely reported.