Despite the importance of menstruation and the menstrual cycle to health, human rights, and sociocultural and economic wellbeing, the study of menstrual health suffers from a lack of funding, and research remains fractured across many disciplines. We sought to systematically review approaches to measure four aspects of changes to the menstrual cycle—bleeding, blood, pain, and perceptions— caused by any source and used in any field. We searched MEDLINE, Embase, and four instrument databases and included peer-reviewed articles published between 2006 and 2023 that reported on the development or validation of instruments assessing menstrual changes using quantitative or mixed-methods methodology. We evaluated instruments on measure quality and utility for clinical trials. From a total of 8,490 articles, 8,316 were excluded (i.e., 376 duplicates, 7,704 during title/abstract screening, and 236 during full text review), yielding 94 instruments from 174 included articles. Almost half of articles were from the United States or United Kingdom and over half of instruments were only in English, Spanish, French, or Portuguese. Most instruments measured bleeding, pain, or perceptions, but few assessed blood. Nearly 60% of instruments were developed for populations with menstrual or gynecologic disorders or symptoms. Most instruments had fair or good measure quality and/or clinical trial utility; however, most instruments lacked evidence on responsiveness, question sensitivity and/or transferability, and only three instruments had good scores of both quality and utility. Although we took a novel, broad, and transdisciplinary approach, our systematic review found important gaps in the literature and instrument landscape and a need to examine the menstrual cycle in a more comprehensive, inclusive, and standardized way. Our findings can inform the development of new or modified instruments, which—if used across the many fields that study menstrual health—can contribute to a more systemic and holistic understanding of menstruation and the menstrual cycle.