The epitranscriptome, comprising post-transcriptional RNA modifications, has emerged as a pivotal regulator of gene expression in the female reproductive system. Among these modifications, 5-methylcytosine (m5C) stands out as a widespread and highly conserved mark whose roles in female reproductive health and disease are increasingly recognized but have not yet been systematically summarized. This review aims to synthesize current knowledge on the functions and regulatory mechanisms of m5C in female reproductive physiology and associated pathologies. We begin with a foundational overview of m5C, detailing its definition, biological functions, and the dynamic regulatory network of 'writers,' 'readers,' and 'erasers.' We then examine the critical roles of m5C in key physiological processes, including oogenesis and early embryonic development. Furthermore, we provide an in-depth analysis of the mechanistic involvement and clinical implications of m5C dysregulation in various gynecological diseases. By consolidating recent advances, this review seeks to establish a comprehensive framework for understanding m5C in the female reproductive system and to offer a valuable reference and theoretical basis for future research and therapeutic exploration.