Epilepsy is one of the most challenging neurologic diseases confronted by human society. Approximately 30–40% of the worldwide epilepsy patients are diagnosed with drug-resistant epilepsy and require pre-surgery evaluation. Magnetoencephalography (MEG) is a unique technology that provides optimal spatial-temporal resolution and has become a powerful non-invasive imaging modality that can localize the interictal spikes and guide the implantation of intracranial electrodes. Currently, the most widely used MEG source estimation method for clinical applications is equivalent current dipoles (ECD). However, ECD has difficulties in precisely locating deep sources such as insular lobe. In contrast to ECD, another MEG source estimation method named spatio-temporal unifying tomography (STOUT) with spatial sparsity has particular advantages in locating deep sources. In this case study, we recruited a 5 year-old female patient with insular lobe epilepsy and her seizure recurred in 1 year after receiving the radiofrequency thermocoagulation (RF-TC) therapy. The STOUT method was adopted to locate deep sources for identifying the epileptic foci in epilepsy evaluation. MEG STOUT method strongly supported a stereo-electroencephalographic (SEEG)-guided RF-TC operation, and the patient reported a satisfactory therapeutic effect. This case raises the possibility that STOUT method can be used particularly for the localization of deep sources, and successfully conducted RF-TC under the guidance of MEG STOUT results.