Epilepsy is one of the most common neurologic disorders in childhood that often requires long term treatment with antiepileptic drugs. Both antiepileptic treatment and the comorbidities associated with epilepsy have a negative impact on bone health in growing children. Given the fact that vitamin D deficiency is a major public health problem worldwide, clinicians caring for children with chronic diseases should be aware of effects of the medication on the bone metabolism. Yet, vitamin D deficiency due to antiepileptic treatment is an overlooked issue among neurologists. In this review, we briefly describe vitamin D metabolism and the effect of vitamin D in the brain. We also discuss the literature in terms of vitamin D deficiency and antiepileptic treatment in the pediatric population.