Women's health disorders, including polycystic ovary syndrome (PCOS), infertility, dysmenorrhea, menopausal syndrome, and pregnancy-related complications, represent a substantial global health burden. The increasing prevalence of lifestyle-related diseases, obesity, stress, and metabolic dysfunction has created a growing need for holistic and patient-centred healthcare approaches. Ayurveda, the traditional system of medicine of India, offers individualised therapeutic strategies based on constitutional assessment, lifestyle regulation, dietary interventions, and herbal medicines. Despite its widespread use, integration of Ayurveda into mainstream healthcare remains limited due to insufficient high-quality clinical evidence. Designing clinical trials for Ayurvedic interventions presents unique methodological challenges because conventional randomized controlled trial (RCT) frameworks are primarily developed for standardized pharmaceutical interventions, whereas Ayurveda emphasises individualised and multimodal treatment. This review discusses key challenges in Ayurvedic clinical research, including treatment personalisation, intervention standardisation, placebo design, outcome selection, and integration of traditional and biomedical diagnostic systems. Emerging methodological approaches such as pragmatic clinical trials, whole-systems research, N-of-1 studies and real-world evidence generation are examined as potential solutions. Ethical considerations, regulatory requirements, digital health technologies, and artificial intelligence applications are also discussed. Developing scientifically rigorous yet context-sensitive research methodologies is essential for generating robust evidence and facilitating the integration of Ayurveda into contemporary women's healthcare.