Background: Vitamin D deficiency is not only associated with the adverse effects of chronic treatment with antiepileptic drugs (AEDs), but also with epilepsy. Although emerging evidence suggests that AEDs can accelerate the vitamin D catabolism, resulting in suboptimal vitamin D status, there are a limited number of studies examining the vitamin D status in epileptic patients, especially in first-episode or AEDs-naïve children. Methods: Determined with high-performance liquid chromatography-tandem mass spectrometry, circulating 25(OH)D3 and 24,25(OH)2D3 levels, and 24,25(OH)2D3:25(OH)D3 ratio were compared between AEDs-treated epileptic (n = 363) and control (n = 159) children. To further figure out whether the patients were in a vitamin D deficient prone state even before treatment, epileptic children before their initiation of treatment (n = 51) were enrolled into a follow-up study. Results: A significant decrease of 25(OH)D3 and 24,25(OH)2D3 levels, but a significant increase of 24,25(OH)2D3:25(OH)D3 ratio was observed in epileptic children, compared with controls. Baseline 25(OH)D3, 24,25(OH)2D3 and 24,25(OH)2D3:25(OH)D3 ratio in the follow-up group were similar to those in controls, but significantly changed with 2 months of AED therapy. Conclusions: Disturbed vitamin D levels were possibly the consequence of AED therapy, rather than the contributing factor of epilepsy. Collectively, circulating vitamin D levels should be monitored and corrected in AEDs-treated epileptic children.