SummaryPurpose:  In the presurgical evaluation of children and juvenile patients with refractory focal epilepsy, the main challenge is to localize the point of seizure onset as precisely as possible. We compared results of the conventional electroencephalography–functional magnetic resonance imaging (EEG‐fMRI) analysis with those obtained with a newly developed method using voltage maps of average interictal epileptiform discharges (IEDs) recorded during clinical long‐term monitoring and with the results of the electric source imaging (ESI).Methods:  Simultaneous EEG‐fMRI was recorded in nine patients (ages 1.5–17.5 years) undergoing presurgical evaluation. The postoperative outcome and resected area were compared with the following: the localizations of blood oxygen–level dependent (BOLD) signal changes associated with IEDs, which were identified by visual inspection changes using SPM5 software (Analysis I); BOLD signal changes related to IED topography, which was characterized using spike‐specific voltage maps of average IED recorded outside the MR scanner during clinical long‐term monitoring (Analysis II); as well as results of EEG source analysis based on the distributed linear local autoregressive average (LAURA) algorithm using the Cartool software by Denis Brunet (Analysis III).Key Findings:  All nine patients had postoperative outcome Engel class I–IIb (postoperative time 6–26 months). The analysis I revealed an IED‐related area of activation within the resection area in 3 (33%) of 9 patients, analysis II was able to reliably localize the source of epileptic activity in 4 (44%) of 9 patients, and analysis III rendered results concordant with the postoperative resection site in all nine patients.Conclusions:  The localization of seizure onset based on EEG‐fMRI may be a useful adjunct in the preoperative evaluation but also has some deficits that impair the reliability of results. In contrast, EEG source analysis is clearly a more credible method for epileptic focus localization in children with refractory epilepsies. It seems likely that the analysis based on IED topography (Analysis II) may increase sensitivity and reliability of EEG‐fMRI in some patients. However, the benefit from this innovative method in children is rather limited compared with adults.