Melatonin, a potent antioxidant and free radical scavenger, has been demonstrated to be effective in gynecological conditions and female reproductive cancers. This review consolidates the accumulating evidence on melatonin's multifaceted protective effects in different pathological contexts. In gynecological conditions such as endometriosis, polycystic ovary syndrome (PCOS), and uterine leiomyoma, melatonin has shown promising effects in reducing oxidative stress, inflammation, and hormonal imbalances. It inhibits adhesion molecules' production, and potentially mitigates leukocyte adherence and inflammatory responses. Melatonin's regulatory effects on hormone production and insulin sensitivity in PCOS individuals make it a promising candidate for improving oocyte quality and menstrual irregularities. Moreover, melatonin exhibits significant antitumor effects by modulating various signaling pathways, promoting apoptosis, and suppressing metastasis in breast cancers and gynecological cancers, including ovarian, endometrial, and cervical cancers. Furthermore, melatonin's protective effects are suggested to be mediated by interactions with its receptors, estrogen receptors and other nuclear receptors. The regulation of clock-related genes and circadian clock systems may also contribute to its inhibitory effects on cancer cell growth. However, more comprehensive research is warranted to fully elucidate the underlying molecular mechanisms and establish melatonin as a potential therapeutic agent for these conditions.