Presurgical functional mapping in epilepsy surgery is critical, and nTMS is a well-suited noninvasive tool to evaluate motor, speech, and language functions in the individuals with refractory epilepsy of various etiologies. nTMS is especially useful in young children in whom most other modalities are frequently unsuccessful. The functional mapping procedures in refractory epilepsy are similar to the recommended protocol for adult brain tumor patients and healthy volunteers. However, modifications are warranted to accommodate younger age, antiseizure medications, seizure type and frequency, and range of cognitive/compliance abilities unique to this cohort. nTMS-derived localization of motor cortex has excellent agreement with electrical stimulation mapping. Along with localization of critical eloquent cortices, speech and language mapping with nTMS allows for determining hemispheric dominance for language. Speech and language areas identified by nTMS exhibit moderate agreement with electrical stimulation mapping. Consistent with the reports in brain tumor patients, speech and language mapping with nTMS in epilepsy cohort suffers from excessive false-positive but excellent true-negative results. nTMS in epilepsy cohort has excellent safety profile and has the potential for being an effective treatment for refractory epilepsy.