There has been significant progress in some areas of women’s health in Malaysia, notably in reducing maternal mortality but this rate has remained static in recent years. Rapid urbanization and an obesogenic environment have contributed to the steady increase in diabetes, obesity and cancers in Malaysian women. In addition to the rising non communicable diseases, significant knowledge gaps remain for reproductive health in this country with limited data on what would be expected to be common conditions such as endometriosis, pelvic pain, infertility, incontinence and polycystic ovary syndrome. Amidst the growing plethora of topic areas in women’s health, it is unclear which should be prioritised for immediate research investments. The aim of this study was to understand the gaps and opportunities in women’s health translational research in Malaysia. This priority-setting exercise identified the key values, principles and research priorities for women’s health in Malaysia through the engagement of health professionals and women with lived experience through a modified Delphi and Nominal Group Technique. Five principles and values and eight priorities were identified. The highest ranked value and principle for women’s health was community education that addresses health literacy, engagement and empowerment, which uphold the autonomy and dignity of women. The highest-ranked health priority was diabetes, which includes healthy weight and lifestyle. Gaps and opportunities include building intersectoral partnerships, addressing equitable access to reproductive services, integrating data systems to enable access, and strengthening research support services such as biostatistics, health economics, legal, financial and ethical support. Addressing these gaps and opportunities would accelerate progress in women's translational health research in Malaysia.