Objectives The COVID-19 pandemic threatens to widen existing gender inequities worldwide. A growing body of literature assesses the harmful consequences of public health emergencies (PHEs) for women and girls; however, evidence of what works to alleviate such impacts is limited. To inform viable mitigation strategies, we reviewed the evidence on gender-based interventions implemented in PHEs, including disease outbreaks and natural disasters. Methods We conducted a rapid scoping review to identify eligible studies by systematically searching the databases MEDLINE, Global Health and Web of Science with the latest search update on 28 May 2021. We used the Sustainable Development Goals as a guiding framework to identify eligible outcomes of gender (in)equality. Results Out of 13 920 records, 16 studies met our eligibility criteria. These included experimental (3), cohort (2), case-control (3) and cross-sectional (9) studies conducted in the context of natural disasters (earthquakes, droughts and storms) or epidemics (Zika, Ebola and COVID-19). Six studies were implemented in Asia, seven in North/Central America and three in Africa. Interventions included economic empowerment programmes (5); health promotion, largely focused on reproductive health (10); and a postearthquake resettlement programme (1). Included studies assessed gender-based outcomes in the domains of sexual and reproductive health, equal opportunities, access to economic resources, violence and health. There was a dearth of evidence for other outcome domains relevant to gender equity such as harmful practices, sanitation and hygiene practices, workplace discrimination and unpaid work. Economic empowerment interventions showed promise in promoting women's and girls' economic and educational opportunities as well as their sexual and reproductive health during PHEs. However, some programme beneficiaries may be at risk of experiencing unintended harms such as an increase in domestic violence. Focused reproductive health promotion may also be an effective strategy for supporting women's sexual and reproductive health, although additional experimental evidence is needed. Conclusions This study identified critical evidence gaps to guide future research on approaches to alleviating gender inequities during PHEs. We further highlight that interventions to promote gender equity in PHEs should take into account possible harmful side effects such as increased gender-based violence. Review registration DOI 10.17605/OSF.IO/8HKFD.