Medicinal plants are an abundant source of secondary metabolites with diverse structures, offering significant potential for the discovery and development of new therapeutic agents. Traditionally, plant-derived compounds have made substantial contributions to modern medicine by providing key molecules—often serving as reference compounds—for the treatment of infectious diseases, cancer, cardiovascular conditions, inflammation, and neurological disorders. The transition from traditional medical use to scientifically validated drug candidates requires a systematic understanding of phytochemical composition, pharmacological activity, molecular mechanisms, pharmacokinetic behavior, and safety profiles. Recent advancements in analytical chemistry, metabolomics, high-throughput screening, molecular docking, molecular dynamics simulations, and artificial intelligence have greatly contributed to the discovery of plant-based therapeutic agents. Primary focus is placed on fundamental phytochemical groups—including alkaloids, flavonoids, terpenoids, phenolic acids, tannins, and glycosides—and their interactions with key molecular targets involved in disease pathogenesis. Chromatographic and spectroscopic techniques, such as HPLC, GC–MS, LC–MS/MS, NMR, and FTIR, have been evaluated in this context to identify chemical compounds and achieve chemical standardization. Despite significant progress, various challenges—related to botanical authentication, phytochemical variability, bioavailability, toxicity, reproducibility, and clinical translation—continue to hinder the development of plant-derived drugs.