Neocortical resective surgery offers a curative option for children with intractable focal epilepsy or brain tumors. Current invasive and noninvasive techniques used for preoperative localization of the eloquent cortex, while critical to prevent potential functional deficits following resective surgery, pose significant challenges in young patients. Neuronavigated transcranial magnetic stimulation (nTMS) is a safe and efficient noninvasive modality for preoperative planning of epilepsy surgery and brain tumor resection in adults. Children are not small adults; however, and modifications may be necessary to ensure the safety and feasibility of nTMS applications in pediatric populations. Preliminary applications of preoperative nTMS in children have been well-received, offering a functional mapping modality that is otherwise unattainable in this delicate population. Here we explore the successful integration of nTMS in pediatric neurosurgery in cases of brain tumors and intractable epilepsy. We also highlight special considerations, such as age, cognitive and developmental limitations, and stimulation parameters, pertinent to the success of nTMS applications in children.