Evidence shows that infectious disease outbreaks are not gender-neutral, meaning that women, men, and gender minorities are differentially affected. This evidence affirms the need to better incorporate a gender lens into infectious disease outbreaks. Despite this evidence, there has been a historic neglect of gender-based analysis in health, including during health crises. Recognizing the lack of available evidence on gender and pandemics, in early 2020 the [Name retracted] project set out to use a gender analysis matrix to conduct rapid, real-time analyses while the pandemic was unfolding to examine the gendered effects of the COVID-19 pandemic. This paper reports on what a gender analysis matrix is, how it can be used to systematically conduct a gender analysis, how it was implemented within the study, ways in which the findings from the matrix were applied and built upon, and challenges encountered when using the matrix methodology.