Next-generation sequencing (NGS) has fundamentally reshaped the diagnostic and therapeutic landscape of gynecologic oncology, bridging the gap between histopathology and precision medicine. By enabling rapid, high-throughput profiling of tumor and germline DNA, NGS allows the identification of driver mutations, actionable alterations, and hereditary cancer syndromes that inform risk assessment, prognostication, and treatment selection. In endometrial carcinoma, The Cancer Genome Atlas (TCGA) has defined four molecular subgroups—POLE-ultramutated, microsatellite instability-high (MMRd), copy-number low (NSMP), and copy-number high/p53-abnormal—revolutionizing risk stratification and adjuvant therapy decisions, as reflected in the 2023 FIGO staging revision. In ovarian cancer, germline and somatic BRCA mutations, along with broader homologous recombination deficiency (HRD), predict sensitivity to platinum-based chemotherapy and PARP inhibitors, while HRD testing is expanding to identify patients beyond classical BRCA carriers. Cervical cancer displays histotype-specific genomic alterations, with PIK3CA, PTEN, KRAS, and ERBB2 mutations emerging as potential therapeutic targets, and HPV integration driving TP53 and RB1 inactivation. Beyond tissue-based testing, innovations such as liquid biopsy, digital pathology, and AI-powered multi-omics are shaping the future of molecular diagnostics. Circulating tumor DNA (ctDNA) enables real-time monitoring of minimal residual disease (MRD), detection of resistance mutations, and dynamic tracking of tumor evolution. Digital pathology and artificial intelligence promise automated histologic quantification, molecular prediction from morphology, and integration with genomic data for real-time decision support in tumor boards. Despite transformative potential, the widespread clinical adoption of NGS faces technical, biological, economic, and ethical challenges, including tumor heterogeneity, sample quality limitations, high costs, disparities in access, and complex management of incidental findings or variants of uncertain significance. As sequencing technologies advance and costs decline, integrating real-time tumor profiling, longitudinal liquid biopsy, and AI-driven interpretation will maximize the clinical impact of NGS, establishing it as a cornerstone of personalized care in gynecologic oncology.