Ischemic stroke is a disease associated with high morbidity and disability rates; however, its pathogenesis remains elusive, and treatment options are limited. Ferroptosis, an iron-dependent form of cell death, represents a novel avenue for investigation. The objective of this study was to explore the role of melatonin in MCAO-induced ferroptosis and elucidate its underlying molecular mechanism. To simulate brain damage and neuronal injury caused by ischemic stroke, we established a mouse model of MCAO and an HT-22 cell model of OGD/R. The therapeutic efficacy of melatonin was assessed through measurements of infarct size, brain edema, and neurological scores. Additionally, qRT-PCR, WB analysis, and Co-IP assays were employed to investigate the impact of melatonin on ferroptosis markers such as NCOA4 and FTH1 expression levels. Confocal microscopy was utilized to confirm the colocalization between ferritin and lysosomes. Furthermore, we constructed a SIRT6 siRNA model to validate the regulatory effect exerted by SIRT6 on NCOA4 as well as their binding interaction. The present study provides initial evidence that melatonin possesses the ability to mitigate neuronal damage induced by MCAO and OGD/R. Assessment of markers for oxidative damage and ferroptosis revealed that melatonin effectively inhibits intracellular Fe2+ levels, thereby suppressing ferroptosis. Additionally, our findings demonstrate that melatonin modulates the interaction between FTH1 and NCOA4 via SIRT6, influencing ferritin autophagy without affecting cellular macroautophagy. These findings provide reliable data support for the promotion and application of melatonin in clinical practice.