Magnetoencephalography (MEG) provides accurate localizing information of the epileptogenic zones in localization-related epilepsies. Refractory status epilepticus (RSE) is a life-threatening emergency that often requires prolonged high-dose suppressive therapy (HDST) to stop frequent and prolonged seizures. Surgical treatments for patients with RSE secondary to pre-existing epilepsy were reported. This article addresses the role of MEG in localizing the epileptogenic zone for the surgical treatment of patients with RSE. Five pediatric patients with RSE underwent epilepsy surgery using MEG, scalp video EEG and magnetic resonance imaging (MRI). Ictal MEG spike sources (MEGSSs) were localized in the clustered interictal MEGSSs in right Rolandic region (patient 3) and right temporal region (patient 5). Interictal MEG revealed unilateral clustered MEGSSs in four patients (patients 1, 2, 4, and 5) and bilateral (patient 3). Ictal-onset EEG findings were localized to one region in three patients (patients 1, 3, and 5) and two regions in the other two patients (patients 2 and 4). In all five patients, interictal discharges were widespread involving over two lobes (patients 2 and 4) or three lobes (patients 1, 3, and 5). Suppression burst pattern was obtained by HDST (patient 5). MRI showed cortical dysplasia in three patients (patients 1, 3, and 4). Patient 2 had a normal MRI. Patient 5 had normal MRI at the onset. Repeat MRI 5 days later showed diffusion restriction in the right hippocampus associated with increased signal intensity on T2 and FLAIR sequences. We performed cortical excision in two patients (patients 1 and 4), hemispherectotomy one (patient 3) and anterior temporal lobectomy two patients (patients 2 and 5). Two patients (patients 1 and 3) became seizure free, the other three patients experienced residual seizures. MEG showed clustered MEGSSs during the RSE in the pre-existing epilepsy patients and at an early time window in the acute symptomatic RSE patients. The complete resection of clustered MEGSSs can control RSE and possibly lead to a seizure free outcome.